Merge remote-tracking branch 'origin/master' into ld-20230131-subscription-validating-interceptor-remove-deprecated-methods

hapi-deployable-pom/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		 <groupId>ca.uhn.hapi.fhir</groupId>
 		 <artifactId>hapi-fhir</artifactId>
-		 <version>6.5.0-SNAPSHOT</version>
+		 <version>6.5.1-SNAPSHOT</version>
 		 <relativePath>../pom.xml</relativePath>
 	 </parent>
 

hapi-fhir-android/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-bom/pom.xml

@@ -4,14 +4,14 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>ca.uhn.hapi.fhir</groupId>
 	<artifactId>hapi-fhir-bom</artifactId>
-	<version>6.5.0-SNAPSHOT</version>
+	<version>6.5.1-SNAPSHOT</version>
 	<packaging>pom</packaging>
 	<name>HAPI FHIR BOM</name>
 
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-checkstyle/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-cli/hapi-fhir-cli-api/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseApp.java

@@ -186,6 +186,7 @@ public abstract class BaseApp {
 		commands.add(new ExportConceptMapToCsvCommand());
 		commands.add(new ImportCsvToConceptMapCommand());
 		commands.add(new HapiFlywayMigrateDatabaseCommand());
+		commands.add(new HapiClearMigrationLockCommand());
 		commands.add(new CreatePackageCommand());
 		commands.add(new BulkImportCommand());
 		commands.add(new ReindexTerminologyCommand());

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseClearMigrationLockCommand.java

@@ -0,0 +1,92 @@
+package ca.uhn.fhir.cli;
+
+/*-
+ * #%L
+ * HAPI FHIR - Command Line Client - API
+ * %%
+ * Copyright (C) 2014 - 2023 Smile CDR, Inc.
+ * %%
+ * 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.i18n.Msg;
+import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
+import ca.uhn.fhir.jpa.migrate.HapiMigrator;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+
+import java.util.Arrays;
+import java.util.stream.Collectors;
+
+/**
+ *
+ */
+public abstract class BaseClearMigrationLockCommand extends BaseCommand {
+
+	public static final String CLEAR_LOCK = "clear-migration-lock";
+	private String myMigrationTableName;
+
+	@Override
+	public String getCommandDescription() {
+		return "This command clears a database migration lock";
+	}
+
+
+	@Override
+	public String getCommandName() {
+		return CLEAR_LOCK;
+	}
+
+	@Override
+	public Options getOptions() {
+		Options retVal = new Options();
+		addRequiredOption(retVal, "u", "url", "URL", "The JDBC database URL");
+		addRequiredOption(retVal, "n", "username", "Username", "The JDBC database username");
+		addRequiredOption(retVal, "p", "password", "Password", "The JDBC database password");
+		addRequiredOption(retVal, "d", "driver", "Driver", "The database driver to use (Options are " + driverOptions() + ")");
+		addRequiredOption(retVal, "l", "lock-uuid", "Lock UUID", "The UUID value of the lock held in the database.");
+		return retVal;
+	}
+
+	private String driverOptions() {
+		return Arrays.stream(DriverTypeEnum.values()).map(Enum::name).collect(Collectors.joining(", "));
+	}
+
+	@Override
+	public void run(CommandLine theCommandLine) throws ParseException {
+
+		String url = theCommandLine.getOptionValue("u");
+		String username = theCommandLine.getOptionValue("n");
+		String password = theCommandLine.getOptionValue("p");
+		String lockUUID = theCommandLine.getOptionValue("l");
+		DriverTypeEnum driverType;
+		String driverTypeString = theCommandLine.getOptionValue("d");
+		try {
+			driverType = DriverTypeEnum.valueOf(driverTypeString);
+		} catch (Exception e) {
+			throw new ParseException(Msg.code(2774) + "Invalid driver type \"" + driverTypeString + "\". Valid values are: " + driverOptions());
+		}
+
+
+		DriverTypeEnum.ConnectionProperties connectionProperties = driverType.newConnectionProperties(url, username, password);
+		HapiMigrator migrator = new HapiMigrator(myMigrationTableName, connectionProperties.getDataSource(), driverType);
+		migrator.clearMigrationLockWithUUID(lockUUID);
+	}
+
+
+	protected void setMigrationTableName(String theMigrationTableName) {
+		myMigrationTableName = theMigrationTableName;
+	}
+}

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/HapiClearMigrationLockCommand.java

@@ -0,0 +1,33 @@
+package ca.uhn.fhir.cli;
+
+/*-
+ * #%L
+ * HAPI FHIR - Command Line Client - API
+ * %%
+ * Copyright (C) 2014 - 2023 Smile CDR, Inc.
+ * %%
+ * 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.SchemaMigrator;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.ParseException;
+
+public class HapiClearMigrationLockCommand extends BaseClearMigrationLockCommand {
+	@Override
+	public void run(CommandLine theCommandLine) throws ParseException {
+		setMigrationTableName(SchemaMigrator.HAPI_FHIR_MIGRATION_TABLENAME);
+		super.run(theCommandLine);
+	}
+}

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

@@ -1,31 +0,0 @@
-package ca.uhn.fhir.cli;
-import org.junit.jupiter.api.AfterEach;
-import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.Test;
-import java.io.ByteArrayOutputStream;
-import java.io.PrintStream;
-
-import static org.hamcrest.CoreMatchers.containsString;
-import static org.hamcrest.MatcherAssert.assertThat;
-
-public class BaseAppTest {
-
-	private final PrintStream standardOut = System.out;
-	private final ByteArrayOutputStream outputStreamCaptor = new ByteArrayOutputStream();
-
-	@BeforeEach
-	public void setUp() {
-		System.setOut(new PrintStream(outputStreamCaptor));
-	}
-
-	@AfterEach
-	public void tearDown() {
-		System.setOut(standardOut);
-	}
-
-	@Test
-	public void testHelpOption() {
-		App.main(new String[]{"help", "create-package"});
-		assertThat(outputStreamCaptor.toString().trim(), outputStreamCaptor.toString().trim(), containsString("Usage"));
-	}
-}

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

@@ -0,0 +1,32 @@
+package ca.uhn.fhir.cli;
+
+import org.apache.commons.io.output.TeeOutputStream;
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.BeforeEach;
+
+import java.io.ByteArrayOutputStream;
+import java.io.PrintStream;
+
+/**
+ * This class splits output stream to both STDOUT, and a capturing byte array output stream, which can later be inspected.
+ */
+public class ConsoleOutputCapturingBaseTest {
+
+	protected final ByteArrayOutputStream outputStreamCaptor = new ByteArrayOutputStream();
+	protected final TeeOutputStream myTeeOutputStream = new TeeOutputStream(System.out, outputStreamCaptor);
+
+	@BeforeEach
+	public void setUp() {
+		System.setOut(new PrintStream(myTeeOutputStream));
+	}
+
+	@AfterEach
+	public void tearDown() {
+		outputStreamCaptor.reset();
+		System.setOut(System.out);
+	}
+	protected String getConsoleOutput() {
+		return outputStreamCaptor.toString().trim();
+	}
+
+}

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

@@ -0,0 +1,313 @@
+package ca.uhn.fhir.cli;
+
+import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
+import ca.uhn.fhir.jpa.migrate.dao.HapiMigrationDao;
+import ca.uhn.fhir.jpa.migrate.entity.HapiMigrationEntity;
+import ca.uhn.fhir.system.HapiSystemProperties;
+import com.google.common.base.Charsets;
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.IOUtils;
+import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.springframework.jdbc.core.JdbcTemplate;
+import org.springframework.jdbc.core.support.AbstractLobCreatingPreparedStatementCallback;
+import org.springframework.jdbc.support.lob.DefaultLobHandler;
+import org.springframework.jdbc.support.lob.LobCreator;
+
+import javax.annotation.Nonnull;
+import java.io.File;
+import java.io.IOException;
+import java.sql.PreparedStatement;
+import java.sql.SQLException;
+import java.sql.Timestamp;
+import java.sql.Types;
+import java.util.*;
+
+import static ca.uhn.fhir.jpa.migrate.HapiMigrationLock.LOCK_PID;
+import static ca.uhn.fhir.jpa.migrate.HapiMigrationStorageSvc.LOCK_TYPE;
+import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.hamcrest.CoreMatchers.containsString;
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.junit.jupiter.api.Assertions.*;
+import static org.slf4j.LoggerFactory.getLogger;
+
+public class HapiClearMigrationLockCommandTest extends ConsoleOutputCapturingBaseTest {
+	
+	private static final Logger ourLog = getLogger(HapiClearMigrationLockCommandTest.class);
+
+	public static final String DB_DIRECTORY = "target/h2_test";
+
+	static {
+		HapiSystemProperties.enableTestMode();
+	}
+
+	@Test
+	public void testClearNonExistingLockIncorrectLock() throws IOException {
+		ConnectionData connectionData = createSchemaAndMigrate("test_migrate_clear_incorrect_lock");
+		HapiMigrationDao dao = new HapiMigrationDao(connectionData.connectionProperties.getDataSource(), DriverTypeEnum.H2_EMBEDDED, "FLY_HFJ_MIGRATION");
+		String correctLockUUID = UUID.randomUUID().toString();
+		String incorrectLockUUID = UUID.randomUUID().toString();
+		createAndSaveLockRow(correctLockUUID, dao);
+
+		String[] args = new String[]{
+			BaseClearMigrationLockCommand.CLEAR_LOCK,
+			"-d", "H2_EMBEDDED",
+			"-u", connectionData.url,
+			"-n", "",
+			"-p", "",
+			"-l", incorrectLockUUID
+		};
+
+		int beforeClearMigrationCount = dao.findAll().size();
+		try {
+			App.main(args);
+			fail();
+		} catch (CommandFailureException e) {
+			assertThat(e.getMessage(), containsString("HAPI-2152: Internal error: on unlocking, a competing lock was found"));
+		}
+	}
+	@Test
+	public void testClearNonExistingLockNoLocks() throws IOException {
+		ConnectionData connectionData = createSchemaAndMigrate("test_migrate_clear_nonexisting_lock");
+		HapiMigrationDao dao = new HapiMigrationDao(connectionData.connectionProperties.getDataSource(), DriverTypeEnum.H2_EMBEDDED, "FLY_HFJ_MIGRATION");
+		String lockUUID = UUID.randomUUID().toString();
+
+		String[] args = new String[]{
+			BaseClearMigrationLockCommand.CLEAR_LOCK,
+			"-d", "H2_EMBEDDED",
+			"-u", connectionData.url,
+			"-n", "",
+			"-p", "",
+			"-l", lockUUID
+		};
+
+		int beforeClearMigrationCount = dao.findAll().size();
+		App.main(args);
+		int afterClearMigrationCount = dao.findAll().size();
+		int removedRows = beforeClearMigrationCount - afterClearMigrationCount;
+		assertEquals(0, removedRows);
+		assertThat(getConsoleOutput(), containsString("Did not successfully remove lock entry. [uuid="+ lockUUID +"]"));
+	}
+	@Test
+	public void testMigrateAndClearExistingLock() throws IOException, SQLException {
+		ConnectionData connectionData = createSchemaAndMigrate("test_migrate_clear_existing_lock");
+		HapiMigrationDao dao = new HapiMigrationDao(connectionData.connectionProperties.getDataSource(), DriverTypeEnum.H2_EMBEDDED, "FLY_HFJ_MIGRATION");
+		String lockUUID = UUID.randomUUID().toString();
+		createAndSaveLockRow(lockUUID, dao);
+
+
+		String[] args = new String[]{
+			BaseClearMigrationLockCommand.CLEAR_LOCK,
+			"-d", "H2_EMBEDDED",
+			"-u", connectionData.url,
+			"-n", "",
+			"-p", "",
+			"-l", lockUUID
+		};
+		int beforeClearMigrationCount = dao.findAll().size();
+		App.main(args);
+		int afterClearMigrationCount = dao.findAll().size();
+		int removedRows = beforeClearMigrationCount - afterClearMigrationCount;
+
+		assertEquals(1, removedRows);
+		assertThat(getConsoleOutput(), containsString("Successfully removed lock entry. [uuid="+ lockUUID +"]"));
+	}
+
+	private record ConnectionData(DriverTypeEnum.ConnectionProperties connectionProperties, String url) {}
+	public ConnectionData createSchemaAndMigrate(String theDbName) throws IOException {
+
+		File location = getLocation(theDbName);
+
+		String url = "jdbc:h2:" + location.getAbsolutePath();
+		DriverTypeEnum.ConnectionProperties connectionProperties = DriverTypeEnum.H2_EMBEDDED.newConnectionProperties(url, "", "");
+		String initSql = "/persistence_create_h2_340.sql";
+		executeSqlStatements(connectionProperties, initSql);
+
+		seedDatabase340(connectionProperties);
+
+		ourLog.info("**********************************************");
+		ourLog.info("Done Setup, Starting Migration...");
+		ourLog.info("**********************************************");
+
+		String[] args = new String[]{
+			BaseFlywayMigrateDatabaseCommand.MIGRATE_DATABASE,
+			"-d", "H2_EMBEDDED",
+			"-u", url,
+			"-n", "",
+			"-p", "",
+			"-r"
+		};
+		App.main(args);
+		return new ConnectionData(connectionProperties, url);
+	}
+
+
+
+
+	private static void createAndSaveLockRow(String theLockUUID, HapiMigrationDao theDao) {
+		HapiMigrationEntity me = new HapiMigrationEntity();
+		me.setPid(LOCK_PID);
+		me.setChecksum(100);
+		me.setDescription(theLockUUID);
+		me.setSuccess(true);
+		me.setExecutionTime(20);
+		me.setInstalledBy("gary");
+		me.setInstalledOn(new Date());
+		me.setVersion("2023.1");
+		me.setType(LOCK_TYPE);
+		theDao.save(me);
+	}
+
+	@Nonnull
+	private File getLocation(String theDatabaseName) throws IOException {
+		File directory = new File(DB_DIRECTORY);
+		if (directory.exists()) {
+			FileUtils.deleteDirectory(directory);
+		}
+
+		return new File(DB_DIRECTORY + "/" + theDatabaseName);
+	}
+
+	private void seedDatabase340(DriverTypeEnum.ConnectionProperties theConnectionProperties) {
+		theConnectionProperties.getTxTemplate().execute(t -> {
+			JdbcTemplate jdbcTemplate = theConnectionProperties.newJdbcTemplate();
+
+			jdbcTemplate.execute(
+				"insert into HFJ_RESOURCE (RES_DELETED_AT, RES_VERSION, FORCED_ID_PID, HAS_TAGS, RES_PUBLISHED, RES_UPDATED, SP_HAS_LINKS, HASH_SHA256, SP_INDEX_STATUS, RES_LANGUAGE, SP_CMPSTR_UNIQ_PRESENT, SP_COORDS_PRESENT, SP_DATE_PRESENT, SP_NUMBER_PRESENT, SP_QUANTITY_PRESENT, SP_STRING_PRESENT, SP_TOKEN_PRESENT, SP_URI_PRESENT, RES_PROFILE, RES_TYPE, RES_VER, RES_ID) values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)",
+				new AbstractLobCreatingPreparedStatementCallback(new DefaultLobHandler()) {
+					@Override
+					protected void setValues(PreparedStatement thePs, LobCreator theLobCreator) throws SQLException {
+						thePs.setNull(1, Types.TIMESTAMP);
+						thePs.setString(2, "R4");
+						thePs.setNull(3, Types.BIGINT);
+						thePs.setBoolean(4, false);
+						thePs.setTimestamp(5, new Timestamp(System.currentTimeMillis()));
+						thePs.setTimestamp(6, new Timestamp(System.currentTimeMillis()));
+						thePs.setBoolean(7, false);
+						thePs.setNull(8, Types.VARCHAR);
+						thePs.setLong(9, 1L);
+						thePs.setNull(10, Types.VARCHAR);
+						thePs.setBoolean(11, false);
+						thePs.setBoolean(12, false);
+						thePs.setBoolean(13, false);
+						thePs.setBoolean(14, false);
+						thePs.setBoolean(15, false);
+						thePs.setBoolean(16, false);
+						thePs.setBoolean(17, false);
+						thePs.setBoolean(18, false);
+						thePs.setNull(19, Types.VARCHAR);
+						thePs.setString(20, "Patient");
+						thePs.setLong(21, 1L);
+						thePs.setLong(22, 1L);
+					}
+				}
+			);
+
+			jdbcTemplate.execute(
+				"insert into HFJ_RES_VER (RES_DELETED_AT, RES_VERSION, FORCED_ID_PID, HAS_TAGS, RES_PUBLISHED, RES_UPDATED, RES_ENCODING, RES_TEXT, RES_ID, RES_TYPE, RES_VER, PID) values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)",
+				new AbstractLobCreatingPreparedStatementCallback(new DefaultLobHandler()) {
+					@Override
+					protected void setValues(PreparedStatement thePs, LobCreator theLobCreator) throws SQLException {
+						thePs.setNull(1, Types.TIMESTAMP);
+						thePs.setString(2, "R4");
+						thePs.setNull(3, Types.BIGINT);
+						thePs.setBoolean(4, false);
+						thePs.setTimestamp(5, new Timestamp(System.currentTimeMillis()));
+						thePs.setTimestamp(6, new Timestamp(System.currentTimeMillis()));
+						thePs.setString(7, "JSON");
+						theLobCreator.setBlobAsBytes(thePs, 8, "{\"resourceType\":\"Patient\"}".getBytes(Charsets.US_ASCII));
+						thePs.setLong(9, 1L);
+						thePs.setString(10, "Patient");
+						thePs.setLong(11, 1L);
+						thePs.setLong(12, 1L);
+					}
+				}
+			);
+
+			jdbcTemplate.execute(
+				"insert into HFJ_SPIDX_STRING (SP_MISSING, SP_NAME, RES_ID, RES_TYPE, SP_UPDATED, SP_VALUE_EXACT, SP_VALUE_NORMALIZED, SP_ID) values (?, ?, ?, ?, ?, ?, ?, ?)",
+				new AbstractLobCreatingPreparedStatementCallback(new DefaultLobHandler()) {
+					@Override
+					protected void setValues(PreparedStatement thePs, LobCreator theLobCreator) throws SQLException {
+						thePs.setBoolean(1, false);
+						thePs.setString(2, "given");
+						thePs.setLong(3, 1L); // res-id
+						thePs.setString(4, "Patient");
+						thePs.setTimestamp(5, new Timestamp(System.currentTimeMillis()));
+						thePs.setString(6, "ROBERT");
+						thePs.setString(7, "Robert");
+						thePs.setLong(8, 1L);
+					}
+				}
+			);
+
+			jdbcTemplate.execute(
+				"insert into HFJ_SPIDX_TOKEN (SP_MISSING, SP_NAME, RES_ID, RES_TYPE, SP_UPDATED, SP_SYSTEM, SP_VALUE, SP_ID) values (?, ?, ?, ?, ?, ?, ?, ?)",
+				new AbstractLobCreatingPreparedStatementCallback(new DefaultLobHandler()) {
+					@Override
+					protected void setValues(PreparedStatement thePs, LobCreator theLobCreator) throws SQLException {
+						thePs.setBoolean(1, false);
+						thePs.setString(2, "identifier");
+						thePs.setLong(3, 1L); // res-id
+						thePs.setString(4, "Patient");
+						thePs.setTimestamp(5, new Timestamp(System.currentTimeMillis()));
+						thePs.setString(6, "http://foo");
+						thePs.setString(7, "12345678");
+						thePs.setLong(8, 1L);
+					}
+				}
+			);
+
+			jdbcTemplate.execute(
+				"insert into HFJ_SPIDX_DATE (SP_MISSING, SP_NAME, RES_ID, RES_TYPE, SP_UPDATED, SP_VALUE_HIGH, SP_VALUE_LOW, SP_ID) values (?, ?, ?, ?, ?, ?, ?, ?)",
+				new AbstractLobCreatingPreparedStatementCallback(new DefaultLobHandler()) {
+					@Override
+					protected void setValues(PreparedStatement thePs, LobCreator theLobCreator) throws SQLException {
+						thePs.setBoolean(1, false);
+						thePs.setString(2, "birthdate");
+						thePs.setLong(3, 1L); // res-id
+						thePs.setString(4, "Patient");
+						thePs.setTimestamp(5, new Timestamp(System.currentTimeMillis()));
+						thePs.setTimestamp(6, new Timestamp(1000000000L)); // value high
+						thePs.setTimestamp(7, new Timestamp(1000000000L)); // value low
+						thePs.setLong(8, 1L);
+					}
+				}
+			);
+
+
+			return null;
+		});
+
+	}
+
+	private void executeSqlStatements(DriverTypeEnum.ConnectionProperties theConnectionProperties, String theInitSql) throws
+		IOException {
+		String script = IOUtils.toString(HapiClearMigrationLockCommandTest.class.getResourceAsStream(theInitSql), Charsets.UTF_8);
+		List<String> scriptStatements = new ArrayList<>(Arrays.asList(script.split("\n")));
+		for (int i = 0; i < scriptStatements.size(); i++) {
+			String nextStatement = scriptStatements.get(i);
+			if (isBlank(nextStatement)) {
+				scriptStatements.remove(i);
+				i--;
+				continue;
+			}
+
+			nextStatement = nextStatement.trim();
+			while (nextStatement.endsWith(";")) {
+				nextStatement = nextStatement.substring(0, nextStatement.length() - 1);
+			}
+			scriptStatements.set(i, nextStatement);
+		}
+
+		theConnectionProperties.getTxTemplate().execute(t -> {
+			for (String next : scriptStatements) {
+				theConnectionProperties.newJdbcTemplate().execute(next);
+			}
+			return null;
+		});
+
+	}
+
+}
+

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

@@ -0,0 +1,13 @@
+package ca.uhn.fhir.cli;
+import org.junit.jupiter.api.Test;
+
+import static org.hamcrest.CoreMatchers.containsString;
+import static org.hamcrest.MatcherAssert.assertThat;
+
+public class HelpOptionTest extends ConsoleOutputCapturingBaseTest {
+	@Test
+	public void testHelpOption() {
+		App.main(new String[]{"help", "create-package"});
+		assertThat(outputStreamCaptor.toString().trim(), outputStreamCaptor.toString().trim(), containsString("Usage"));
+	}
+}

hapi-fhir-cli/hapi-fhir-cli-app/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-cli</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom</relativePath>
 	</parent>
 

hapi-fhir-cli/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-client-okhttp/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-client/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-converter/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-dist/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-docs/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/Narrative.java

@@ -42,7 +42,7 @@ FhirContext ctx = FhirContext.forDstu2();
 ctx.setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
 
 // Encode the output, including the narrative
-String output = ctx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient);
+String output = ctx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
 System.out.println(output);
 //END SNIPPET: example1
 

hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/NarrativeGenerator.java

@@ -21,6 +21,7 @@ package ca.uhn.hapi.fhir.docs;
  */
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.dstu2.resource.Patient;
 import ca.uhn.fhir.narrative.CustomThymeleafNarrativeGenerator;
 
 @SuppressWarnings("unused")
@@ -33,7 +34,11 @@ FhirContext ctx = FhirContext.forDstu2();
 String propFile = "classpath:/com/foo/customnarrative.properties";
 CustomThymeleafNarrativeGenerator gen = new CustomThymeleafNarrativeGenerator(propFile);
 
+Patient patient = new Patient();
+
 ctx.setNarrativeGenerator(gen);
+String output = ctx.newJsonParser().encodeResourceToString(patient);
+System.out.println(output);
 //END SNIPPET: gen
 
 	

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/3482-unsupported-channel-type-bad-error-messag.yaml

@@ -0,0 +1,4 @@
+type: fix
+issue: 3482
+jira: SMILE-5076
+title: "Previously, persistence modules were attempting to activate subscriptions that used channel types they did not support. This has been changed, and those subscriptions will not be activated if the given channel type is not supported"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4090-mdm-score-null-for-links-with-new-golden-resource.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 4090
+title: "Previously, mdm links that connected resources and golden resources that were newly created had a link score of null,
+this changes it to 1.0 as the golden resource should be a perfect match with the source resource it was created from."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4441-bad-resource-refs-should-not-create.yaml

@@ -0,0 +1,7 @@
+---
+type: fix
+issue: 4441
+title: "Creating a resource with an invalid embedded resource reference
+      would not fail. Even if IsEnforceReferentialIntegrityOnWrite was enabled.
+      This has been fixed, and invalid references will throw.
+      "

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4481-reindex-batch-job-fails-when-processing-deleted-resources.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 4481
+jira: SMILE-4961
+title: "Previously, a reindex batch job would fail when executing on deleted resources.  This issue has been fixed."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4486-mdm-inconsistent-possible-match-scores.yaml

@@ -0,0 +1,3 @@
+type: fix
+issue: 4486
+title: "Previously, some MDM links of type `POSSIBLE_MATCH` were saved with unnormalized score values. This has been fixed."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4491-allow-jobs-in-finalize-to-be-cancelled.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 4491
+title: "Batch2 Jobs in the FINALIZE state can now be
+      cancelled."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4491-move-reduction-step-to-messaging-framework.yaml

@@ -0,0 +1,8 @@
+---
+type: fix
+issue: 4491
+title: "Moved batch2 reduction step logic to the messaging queue.
+      Before it was executed during the maintenance run directly.
+      This resulted in bugs with multiple reduction steps kicking
+      off for long running jobs.
+      "

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/450-update-to-narrative-generation-documentation.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 4520
+jira: SMILE-4406
+title: "Updating documentation related to narrative generation."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4500-ld-20230201-bulk-export-scheduled-delete-completely-non-functional.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 4500
+jira: SMILE-6001
+title: "Schedule bulk export job and binary was not working with relational databases.  This has now been fixed with a reimplementation for batch 2."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4508-unable-to-expunge-codesystems.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 4508
+title: "Deleting CodeSystem resources by URL then expunging would fail to
+ expunge and a foreign key error would be thrown. This has been fixed."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4511-bulk-export-stuck-in-finalize-state.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 4511
+jira: SMILE-6064
+title: "Previously, bulk export jobs were getting stuck in the `FINALIZE` state when performed 
+with many resources and a low Bulk Export File Maximum Capacity. This has been fixed."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4516-clear-migration-lock.yaml

@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 4516
+title: "A new command has been added to the HAPI-FHIR CLI called `clear-migration-lock`. This can be used to fix a database state which can occur if a migration is interrupted before completing."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4526-fix-reduction-step.yaml

@@ -0,0 +1,7 @@
+---
+type: fix
+issue: 4526
+title: "Fixing an issue where a long running reduction step causes
+      the message not to be processed fast enough, thereby allowing
+      multiple reduction step jobs to start.
+      "

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4533-channel-import-null-header-null-pointer-exception.yaml

@@ -0,0 +1,7 @@
+---
+type: fix
+issue: 4533
+jira: SMILE-5554
+title: "Previously, if a message with a null header was sent to a Channel Import module and failed,
+a NullPointerException would occur and the consumer would become unable to receive any further messages.
+This has now been fixed."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4537-message-to-string-redaction.yaml

@@ -0,0 +1,5 @@
+---
+type: change
+issue: 4537
+title: "ResourceDeliveryMessage no longer includes the payload in toString().
+   This avoids leaking sensitive data to logs and other channels."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/model/narrative_generation.md

@@ -2,7 +2,7 @@
 
 HAPI provides several ways to add [Narrative Text](http://hl7.org/fhir/narrative.html) to your encoded messages.
 
-The simplest way is to simply place the narrative text directly in the resource via the `setDivAsString()` method.
+The simplest way is to place the narrative text directly in the resource via the `setDivAsString()` method.
 
 ```java
 {{snippet:classpath:/ca/uhn/hapi/fhir/docs/Narrative.java|simple}}
@@ -18,7 +18,7 @@ HAPI's built-in narrative generation uses the [Thymeleaf](http://www.thymeleaf.o
 
 ## A Simple Example
 
-Activating HAPI's built-in narrative generator is as simple as calling [setNarrativeGenerator](/hapi-fhir/apidocs/hapi-fhir-base/ca/uhn/fhir/context/FhirContext.html#setNarrativeGenerator(ca.uhn.fhir.narrative.INarrativeGenerator).
+Activating HAPI's built-in narrative generator is as simple as calling [setNarrativeGenerator](/hapi-fhir/apidocs/hapi-fhir-base/ca/uhn/fhir/context/FhirContext.html#setNarrativeGenerator(ca.uhn.fhir.narrative.INarrativeGenerator)).
 
 ```java
 {{snippet:classpath:/ca/uhn/hapi/fhir/docs/Narrative.java|example1}}
@@ -54,8 +54,8 @@ Note that these templates expect a few specific CSS definitions to be present in
 
 To use your own templates for narrative generation, simply create one or more templates, using the Thymeleaf HTML based syntax.
 
-```java
+```html
-{{snippet:classpath:/ca/uhn/fhir/narrative/OperationOutcome.html}}
+{{snippet:classpath:/ca/uhn/hapi/fhir/docs/snippet/OperationOutcome.html}}
 ```
 
 Then create a properties file which describes your templates. In this properties file, each resource to be defined has a pair or properties.
@@ -79,13 +79,16 @@ vitalsigns.profile=http://hl7.org/fhir/StructureDefinition/vitalsigns
 vitalsigns.narrative=classpath:com/example/narrative/Observation_Vitals.html
 ```
 
-You may also override/define behaviour for datatypes and other structures. These datatype narrative definitions will be used as content within <code>th:narrative</code> blocks in resource templates. See the example resource template above for an example.
+You may also override/define behaviour for datatypes and other structures. These datatype narrative definitions will be used as content within <code>th:narrative</code> blocks in resource templates. See the [example above](#creating-your-own-templates).
 
 ```properties
 # You can create a template based on a type name
 quantity.dataType=Quantity
 quantity.narrative=classpath:com/example/narrative/Quantity.html
 
+string.dataType=String
+string.narrative=classpath:com/example/narrative/String.html
+
 # Or by class name, which can be useful for custom datatypes and structures
 custom_extension.class=com.example.model.MyCustomExtension
 custom_extension.narrative=classpath:com/example/narrative/CustomExtension.html
@@ -105,13 +108,13 @@ Thymeleaf has a concept called Fragments, which allow reusable template portions
 {{snippet:classpath:ca/uhn/fhir/narrative/narrative-with-fragment.properties}}
 ```
 
-The following template declares a fragment (this is `narrative-with-fragment-child.html` in the example above):
+The following template declares `Fragment1` and `Fragment2` as part of file `narrative-with-fragment-child.html`: 
 
 ```html
 {{snippet:classpath:ca/uhn/fhir/narrative/narrative-with-fragment-child.html}}
 ```
 
-And the following template uses it (this is `narrative-with-fragment-child.html` in the example above):
+And the following parent template (`narrative-with-fragment-parent.html`) imports `Fragment1` with parameter 'blah':
 
 ```html
 {{snippet:classpath:ca/uhn/fhir/narrative/narrative-with-fragment-parent.html}}

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/snippet/OperationOutcome.html

@@ -0,0 +1,23 @@
+
+<html>
+<head>
+   <link rel="stylesheet" type="text/css" href="narrative.css"/>
+</head>
+<body>
+<!--*/-->
+<div>
+   <h1>Operation Outcome</h1>
+   <table border="0">
+      <tr th:each="issue : ${resource.issue}">
+         <td th:text="${issue.severityElement.value}" style="font-weight: bold;"></td>
+         <td th:text="${issue.location}"></td>
+         <td th:narrative="${issue.diagnostics}"></td>
+      </tr>
+   </table>
+</div>
+
+<!--*/-->
+</body>
+</html>
+
+

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/tools/hapi_fhir_cli.md

@@ -101,6 +101,22 @@ The `migrate-database` command may be used to Migrate a database schema when upg
 
 See [Upgrading HAPI FHIR JPA](/docs/server_jpa/upgrading.html) for information on how to use this command.
 
+# Clear Migration lock
+
+the `clear-migration-lock` command should be used if an upgrade to HAPI-FHIR failed during a migration. The migration system creates a lock row when it begins. If the migration is cancelled before it finishes, the system will be left in an inconsistent state. In order to resume the migration, the lock row must be removed. From your migration logs, you will see a line which looks like the following: 
+
+```text
+Migration Lock Row added. [uuid=05931c87-c2a4-49d6-8d82-d8ce09fdd8ef]
+```
+
+In order to clear this migration lock, you can run:
+
+```bash
+clear-migration-lock --lock-uuid 05931c87-c2a4-49d6-8d82-d8ce09fdd8ef
+```
+
+
+
 # Reindex Terminology
 
 The `reindex-terminology` command may be used to recreate freetext indexes for terminology resources.

hapi-fhir-jacoco/pom.xml

@@ -11,7 +11,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jaxrsserver-base/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpa/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>

hapi-fhir-jpaserver-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch2/JpaJobPersistenceImpl.java

@@ -29,13 +29,13 @@ import ca.uhn.fhir.batch2.model.MarkWorkChunkAsErrorRequest;
 import ca.uhn.fhir.batch2.model.StatusEnum;
 import ca.uhn.fhir.batch2.model.WorkChunk;
 import ca.uhn.fhir.batch2.models.JobInstanceFetchRequest;
-import ca.uhn.fhir.util.Logs;
 import ca.uhn.fhir.jpa.dao.data.IBatch2JobInstanceRepository;
 import ca.uhn.fhir.jpa.dao.data.IBatch2WorkChunkRepository;
 import ca.uhn.fhir.jpa.entity.Batch2JobInstanceEntity;
 import ca.uhn.fhir.jpa.entity.Batch2WorkChunkEntity;
 import ca.uhn.fhir.jpa.util.JobInstanceUtil;
 import ca.uhn.fhir.model.api.PagingIterator;
+import ca.uhn.fhir.util.Logs;
 import org.apache.commons.collections4.ListUtils;
 import org.apache.commons.lang3.Validate;
 import org.slf4j.Logger;
@@ -59,6 +59,7 @@ import java.util.Set;
 import java.util.UUID;
 import java.util.function.Consumer;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
 
@@ -135,6 +136,12 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
 		return entity.getId();
 	}
 
+	@Override
+	@Transactional(propagation = Propagation.REQUIRES_NEW)
+	public List<JobInstance> fetchInstances(String theJobDefinitionId, Set<StatusEnum> theStatuses, Date theCutoff, Pageable thePageable) {
+		return toInstanceList(myJobInstanceRepository.findInstancesByJobIdAndStatusAndExpiry(theJobDefinitionId, theStatuses, theCutoff, thePageable));
+	}
+
 	@Override
 	@Transactional(propagation = Propagation.REQUIRES_NEW)
 	public List<JobInstance> fetchInstancesByJobDefinitionIdAndStatus(String theJobDefinitionId, Set<StatusEnum> theRequestedStatuses, int thePageSize, int thePageIndex) {
@@ -326,13 +333,21 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
 	}
 
 	/**
+	 * Deprecated, use {@link ca.uhn.fhir.jpa.batch2.JpaJobPersistenceImpl#fetchAllWorkChunksForStepStream(String, String)}
 	 * Note: Not @Transactional because the transaction happens in a lambda that's called outside of this method's scope
 	 */
 	@Override
+	@Deprecated
 	public Iterator<WorkChunk> fetchAllWorkChunksForStepIterator(String theInstanceId, String theStepId) {
 		return new PagingIterator<>((thePageIndex, theBatchSize, theConsumer) -> fetchChunksForStep(theInstanceId, theStepId, theBatchSize, thePageIndex, theConsumer));
 	}
 
+	@Override
+	@Transactional(propagation = Propagation.MANDATORY)
+	public Stream<WorkChunk> fetchAllWorkChunksForStepStream(String theInstanceId, String theStepId) {
+		return myWorkChunkRepository.fetchChunksForStep(theInstanceId, theStepId).map((entity) -> toChunk(entity, true));
+	}
+
 	/**
 	 * Update the stored instance
 	 *

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/BulkDataExportJobSchedulingHelperImpl.java

@@ -20,38 +20,47 @@ package ca.uhn.fhir.jpa.bulk.export.svc;
  * #L%
  */
 
+import ca.uhn.fhir.batch2.api.IJobPersistence;
+import ca.uhn.fhir.batch2.jobs.export.BulkExportAppCtx;
+import ca.uhn.fhir.batch2.jobs.export.models.BulkExportBinaryFileId;
+import ca.uhn.fhir.batch2.model.JobInstance;
+import ca.uhn.fhir.batch2.model.StatusEnum;
+import ca.uhn.fhir.batch2.model.WorkChunk;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
-import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
+import ca.uhn.fhir.jpa.api.model.BulkExportJobResults;
 import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportJobSchedulingHelper;
-import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionDao;
-import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionFileDao;
-import ca.uhn.fhir.jpa.dao.data.IBulkExportJobDao;
-import ca.uhn.fhir.jpa.entity.BulkExportCollectionEntity;
-import ca.uhn.fhir.jpa.entity.BulkExportCollectionFileEntity;
-import ca.uhn.fhir.jpa.entity.BulkExportJobEntity;
 import ca.uhn.fhir.jpa.model.sched.HapiJob;
 import ca.uhn.fhir.jpa.model.sched.IHasScheduledJobs;
 import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
 import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
 import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
+import ca.uhn.fhir.util.Batch2JobDefinitionConstants;
+import ca.uhn.fhir.util.JsonUtil;
+import com.google.common.annotations.VisibleForTesting;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.time.DateUtils;
 import org.hl7.fhir.instance.model.api.IBaseBinary;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.Binary;
 import org.quartz.JobExecutionContext;
 import org.slf4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.PageRequest;
-import org.springframework.data.domain.Pageable;
-import org.springframework.data.domain.Slice;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
 import org.springframework.transaction.support.TransactionTemplate;
 
+import javax.annotation.Nonnull;
 import javax.annotation.PostConstruct;
+import java.time.LocalDateTime;
+import java.time.ZoneId;
 import java.util.Date;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
 import java.util.Optional;
 
 import static org.slf4j.LoggerFactory.getLogger;
@@ -59,26 +68,24 @@ import static org.slf4j.LoggerFactory.getLogger;
 public class BulkDataExportJobSchedulingHelperImpl implements IBulkDataExportJobSchedulingHelper, IHasScheduledJobs {
 	private static final Logger ourLog = getLogger(BulkDataExportJobSchedulingHelperImpl.class);
 
-	@Autowired
+	private final DaoRegistry myDaoRegistry;
-	private DaoRegistry myDaoRegistry;
 
-	@Autowired
+	private final PlatformTransactionManager myTxManager;
-	private IBulkExportCollectionDao myBulkExportCollectionDao;
-
-	@Autowired
-	private IBulkExportCollectionFileDao myBulkExportCollectionFileDao;
-
-	@Autowired
-	private PlatformTransactionManager myTxManager;
 	private TransactionTemplate myTxTemplate;
 
-	@Autowired
+	private final DaoConfig myDaoConfig;
-	private IBulkExportJobDao myBulkExportJobDao;
+	private final BulkExportHelperService myBulkExportHelperSvc;
 
-	@Autowired
+	private final IJobPersistence myJpaJobPersistence;
-	private DaoConfig myDaoConfig;
+
-	@Autowired
+	public BulkDataExportJobSchedulingHelperImpl(DaoRegistry theDaoRegistry, PlatformTransactionManager theTxManager, DaoConfig theDaoConfig, BulkExportHelperService theBulkExportHelperSvc, IJobPersistence theJpaJobPersistence, TransactionTemplate theTxTemplate) {
-	private BulkExportHelperService myBulkExportHelperSvc;
+		myDaoRegistry = theDaoRegistry;
+		myTxManager = theTxManager;
+		myDaoConfig = theDaoConfig;
+		myBulkExportHelperSvc = theBulkExportHelperSvc;
+		myJpaJobPersistence = theJpaJobPersistence;
+		myTxTemplate = theTxTemplate;
+	}
 
 	@PostConstruct
 	public void start() {
@@ -97,15 +104,10 @@ public class BulkDataExportJobSchedulingHelperImpl implements IBulkDataExportJob
 	@Override
 	@Transactional(propagation = Propagation.NEVER)
 	public synchronized void cancelAndPurgeAllJobs() {
-		myTxTemplate.execute(t -> {
+		// This is called by unit test code that also calls ExpungeEverythingService,
-			ourLog.info("Deleting all files");
+		// which explicitly deletes both Batch2WorkChunkEntity and Batch2JobInstanceEntity, as well as ResourceTable, in
-			myBulkExportCollectionFileDao.deleteAllFiles();
+		// which Binary's are stored
-			ourLog.info("Deleting all collections");
+		// Long story short, this method no longer needs to do anything
-			myBulkExportCollectionDao.deleteAllFiles();
-			ourLog.info("Deleting all jobs");
-			myBulkExportJobDao.deleteAllFiles();
-			return null;
-		});
 	}
 
 	/**
@@ -116,51 +118,111 @@ public class BulkDataExportJobSchedulingHelperImpl implements IBulkDataExportJob
 	@Override
 	public void purgeExpiredFiles() {
 		if (!myDaoConfig.isEnableTaskBulkExportJobExecution()) {
+			ourLog.debug("bulk export disabled:  doing nothing");
 			return;
 		}
 
-		Optional<BulkExportJobEntity> jobToDelete = myTxTemplate.execute(t -> {
+		final List<JobInstance> jobInstancesToDelete = myTxTemplate.execute(t ->
-			Pageable page = PageRequest.of(0, 1);
+			myJpaJobPersistence.fetchInstances(Batch2JobDefinitionConstants.BULK_EXPORT,
-			Slice<BulkExportJobEntity> submittedJobs = myBulkExportJobDao.findNotRunningByExpiry(page, new Date());
+				StatusEnum.getEndedStatuses(),
-			if (submittedJobs.isEmpty()) {
+				computeCutoffFromConfig(),
-				return Optional.empty();
+				PageRequest.of(0, 50))
-			}
+		);
-			return Optional.of(submittedJobs.getContent().get(0));
-		});
 
-		if (jobToDelete.isPresent()) {
+		if (jobInstancesToDelete == null || jobInstancesToDelete.isEmpty()) {
-			ourLog.info("Deleting bulk export job: {}", jobToDelete.get());
+			ourLog.debug("No batch 2 bulk export jobs found!  Nothing to do!");
+			ourLog.info("Finished bulk export job deletion with nothing to do");
+			return;
+		}
+
+		for (JobInstance jobInstance : jobInstancesToDelete) {
+			ourLog.info("Deleting batch 2 bulk export job: {}", jobInstance);
 
 			myTxTemplate.execute(t -> {
-				BulkExportJobEntity job = myBulkExportJobDao.getOne(jobToDelete.get().getId());
+				final Optional<JobInstance> optJobInstanceForInstanceId = myJpaJobPersistence.fetchInstance(jobInstance.getInstanceId());
-				for (BulkExportCollectionEntity nextCollection : job.getCollections()) {
-					for (BulkExportCollectionFileEntity nextFile : nextCollection.getFiles()) {
 
-						ourLog.info("Purging bulk data file: {}", nextFile.getResourceId());
+				if (optJobInstanceForInstanceId.isEmpty()) {
-						IIdType id = myBulkExportHelperSvc.toId(nextFile.getResourceId());
+					ourLog.error("Can't find job instance for ID: {} despite having retrieved it in the first step", jobInstance.getInstanceId());
-						getBinaryDao().delete(id, new SystemRequestDetails());
+					return null;
-						getBinaryDao().forceExpungeInExistingTransaction(id, new ExpungeOptions().setExpungeDeletedResources(true).setExpungeOldVersions(true), new SystemRequestDetails());
-						myBulkExportCollectionFileDao.deleteByPid(nextFile.getId());
-
-					}
-
-					myBulkExportCollectionDao.deleteByPid(nextCollection.getId());
 				}
 
-				ourLog.debug("*** About to delete job with ID {}", job.getId());
+				final JobInstance jobInstanceForInstanceId = optJobInstanceForInstanceId.get();
-				myBulkExportJobDao.deleteByPid(job.getId());
+				ourLog.info("Deleting bulk export job: {}", jobInstanceForInstanceId);
+
+				// We need to keep these for investigation but we also need a process to manually delete these jobs once we're done investigating
+				if (StatusEnum.FAILED == jobInstanceForInstanceId.getStatus()) {
+					ourLog.info("skipping because the status is FAILED for ID: {}" + jobInstanceForInstanceId.getInstanceId());
+					return null;
+				}
+
+				purgeBinariesIfNeeded(jobInstanceForInstanceId, jobInstanceForInstanceId.getReport());
+
+				final String batch2BulkExportJobInstanceId = jobInstanceForInstanceId.getInstanceId();
+				ourLog.debug("*** About to delete batch 2 bulk export job with ID {}", batch2BulkExportJobInstanceId);
+
+				myJpaJobPersistence.deleteInstanceAndChunks(batch2BulkExportJobInstanceId);
+
+				ourLog.info("Finished deleting bulk export job: {}", jobInstance.getInstanceId());
+
 				return null;
 			});
 
-			ourLog.info("Finished deleting bulk export job: {}", jobToDelete.get());
+			ourLog.info("Finished deleting bulk export jobs");
 		}
 	}
 
+	private void purgeBinariesIfNeeded(JobInstance theJobInstanceForInstanceId, String theJobInstanceReportString) {
+		final Optional<BulkExportJobResults> optBulkExportJobResults = getBulkExportJobResults(theJobInstanceReportString);
+
+		if (optBulkExportJobResults.isPresent()) {
+			final BulkExportJobResults bulkExportJobResults = optBulkExportJobResults.get();
+			ourLog.debug("job: {} resource type to binary ID: {}", theJobInstanceForInstanceId.getInstanceId(), bulkExportJobResults.getResourceTypeToBinaryIds());
+
+			final Map<String, List<String>> resourceTypeToBinaryIds = bulkExportJobResults.getResourceTypeToBinaryIds();
+			for (String resourceType : resourceTypeToBinaryIds.keySet()) {
+				final List<String> binaryIds = resourceTypeToBinaryIds.get(resourceType);
+				for (String binaryId : binaryIds) {
+					ourLog.info("Purging batch 2 bulk export binary: {}", binaryId);
+					IIdType id = myBulkExportHelperSvc.toId(binaryId);
+					getBinaryDao().delete(id, new SystemRequestDetails());
+				}
+			}
+		} // else we can't know what the binary IDs are, so delete this job and move on
+	}
+
 	@SuppressWarnings("unchecked")
 	private IFhirResourceDao<IBaseBinary> getBinaryDao() {
-		return myDaoRegistry.getResourceDao("Binary");
+		return myDaoRegistry.getResourceDao(Binary.class.getSimpleName());
 	}
 
+	@Nonnull
+	private Optional<BulkExportJobResults> getBulkExportJobResults(String theJobInstanceReportString) {
+		if (StringUtils.isBlank(theJobInstanceReportString)) {
+			ourLog.error(String.format("Cannot parse job report string because it's null or blank: %s", theJobInstanceReportString));
+			return Optional.empty();
+		}
+
+		try {
+			return Optional.of(JsonUtil.deserialize(theJobInstanceReportString, BulkExportJobResults.class));
+		} catch (Exception theException) {
+			ourLog.error(String.format("Cannot parse job report string: %s", theJobInstanceReportString), theException);
+			return Optional.empty();
+		}
+	}
+
+	@Nonnull
+	private Date computeCutoffFromConfig() {
+		final int bulkExportFileRetentionPeriodHours = myDaoConfig.getBulkExportFileRetentionPeriodHours();
+
+		final LocalDateTime cutoffLocalDateTime = LocalDateTime.now()
+			.minusHours(bulkExportFileRetentionPeriodHours);
+
+		return Date.from(cutoffLocalDateTime
+			.atZone(ZoneId.systemDefault())
+			.toInstant());
+	}
+
+
 	public static class PurgeExpiredFilesJob implements HapiJob {
 		@Autowired
 		private IBulkDataExportJobSchedulingHelper myTarget;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/BulkExportCollectionFileDaoSvc.java

@@ -1,41 +0,0 @@
-package ca.uhn.fhir.jpa.bulk.export.svc;
-
-/*-
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2023 Smile CDR, Inc.
- * %%
- * 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.dao.data.IBulkExportCollectionFileDao;
-import ca.uhn.fhir.jpa.entity.BulkExportCollectionFileEntity;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.stereotype.Service;
-
-import org.springframework.transaction.annotation.Transactional;
-
-@Service
-public class BulkExportCollectionFileDaoSvc {
-
-	@Autowired
-	private IBulkExportCollectionFileDao myBulkExportCollectionFileDao;
-
-	@Transactional
-	public void save(BulkExportCollectionFileEntity theBulkExportCollectionEntity) {
-		myBulkExportCollectionFileDao.saveAndFlush(theBulkExportCollectionEntity);
-	}
-
-}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/JpaConfig.java

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.jpa.config;
 
+import ca.uhn.fhir.batch2.api.IJobPersistence;
 import ca.uhn.fhir.batch2.jobs.expunge.DeleteExpungeJobSubmitterImpl;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
@@ -16,6 +17,7 @@ import ca.uhn.fhir.jpa.binary.provider.BinaryAccessProvider;
 import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportJobSchedulingHelper;
 import ca.uhn.fhir.jpa.bulk.export.provider.BulkDataExportProvider;
 import ca.uhn.fhir.jpa.bulk.export.svc.BulkDataExportJobSchedulingHelperImpl;
+import ca.uhn.fhir.jpa.bulk.export.svc.BulkExportHelperService;
 import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
 import ca.uhn.fhir.jpa.bulk.imprt.svc.BulkDataImportSvcImpl;
 import ca.uhn.fhir.jpa.cache.IResourceVersionSvc;
@@ -161,6 +163,7 @@ import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
 import org.springframework.scheduling.TaskScheduler;
 import org.springframework.scheduling.concurrent.ConcurrentTaskScheduler;
 import org.springframework.scheduling.concurrent.ScheduledExecutorFactoryBean;
+import org.springframework.transaction.PlatformTransactionManager;
 
 import javax.annotation.Nullable;
 import java.io.IOException;
@@ -451,8 +454,8 @@ public class JpaConfig {
 	}
 
 	@Bean
-	public IBulkDataExportJobSchedulingHelper bulkDataExportJobSchedulingHelper() {
+	public IBulkDataExportJobSchedulingHelper bulkDataExportJobSchedulingHelper(DaoRegistry theDaoRegistry, PlatformTransactionManager theTxManager, DaoConfig theDaoConfig, BulkExportHelperService theBulkExportHelperSvc, IJobPersistence theJpaJobPersistence) {
-		return new BulkDataExportJobSchedulingHelperImpl();
+		return new BulkDataExportJobSchedulingHelperImpl(theDaoRegistry, theTxManager, theDaoConfig, theBulkExportHelperSvc, theJpaJobPersistence, null);
 	}
 
 	@Bean

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

@@ -681,6 +681,8 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 			// Perform delete
 
+			preDelete(resourceToDelete, entity, theRequest);
+
 			updateEntityForDelete(theRequest, transactionDetails, entity);
 			resourceToDelete.setId(entity.getIdDt());
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IBatch2JobInstanceRepository.java

@@ -28,6 +28,7 @@ import org.springframework.data.jpa.repository.Modifying;
 import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.query.Param;
 
+import java.util.Date;
 import java.util.List;
 import java.util.Set;
 
@@ -60,6 +61,14 @@ public interface IBatch2JobInstanceRepository extends JpaRepository<Batch2JobIns
 		Pageable thePageable
 	);
 
+	@Query("SELECT b from Batch2JobInstanceEntity b WHERE b.myDefinitionId = :defId  AND b.myStatus IN( :stats ) AND b.myEndTime < :cutoff")
+	List<Batch2JobInstanceEntity> findInstancesByJobIdAndStatusAndExpiry(
+		@Param("defId") String theDefinitionId,
+		@Param("stats") Set<StatusEnum> theStatus,
+		@Param("cutoff") Date theCutoff,
+		Pageable thePageable
+	);
+
 	@Query("SELECT e FROM Batch2JobInstanceEntity e WHERE e.myDefinitionId = :jobDefinitionId AND e.myStatus IN :statuses")
 	List<Batch2JobInstanceEntity> fetchInstancesByJobDefinitionIdAndStatus(@Param("jobDefinitionId") String theJobDefinitionId, @Param("statuses") Set<StatusEnum> theIncompleteStatuses, Pageable thePageRequest);
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IBatch2WorkChunkRepository.java

@@ -30,6 +30,7 @@ import org.springframework.data.repository.query.Param;
 
 import java.util.Date;
 import java.util.List;
+import java.util.stream.Stream;
 
 public interface IBatch2WorkChunkRepository extends JpaRepository<Batch2WorkChunkEntity, String>, IHapiFhirJpaRepository {
 
@@ -39,9 +40,16 @@ public interface IBatch2WorkChunkRepository extends JpaRepository<Batch2WorkChun
 	@Query("SELECT DISTINCT e.myStatus from Batch2WorkChunkEntity e where e.myInstanceId = :instanceId AND e.myTargetStepId = :stepId")
 	List<StatusEnum> getDistinctStatusesForStep(@Param("instanceId") String theInstanceId, @Param("stepId") String theStepId);
 
+	/**
+	 * Deprecated, use {@link ca.uhn.fhir.jpa.dao.data.IBatch2WorkChunkRepository#fetchChunksForStep(String, String)}
+	 */
+	@Deprecated
 	@Query("SELECT e FROM Batch2WorkChunkEntity e WHERE e.myInstanceId = :instanceId AND e.myTargetStepId = :targetStepId ORDER BY e.mySequence ASC")
 	List<Batch2WorkChunkEntity> fetchChunksForStep(Pageable thePageRequest, @Param("instanceId") String theInstanceId, @Param("targetStepId") String theTargetStepId);
 
+	@Query("SELECT e FROM Batch2WorkChunkEntity e WHERE e.myInstanceId = :instanceId AND e.myTargetStepId = :targetStepId ORDER BY e.mySequence ASC")
+	Stream<Batch2WorkChunkEntity> fetchChunksForStep(@Param("instanceId") String theInstanceId, @Param("targetStepId") String theTargetStepId);
+
 	@Modifying
 	@Query("UPDATE Batch2WorkChunkEntity e SET e.myStatus = :status, e.myEndTime = :et, e.myRecordsProcessed = :rp, e.mySerializedData = null WHERE e.myId = :id")
 	void updateChunkStatusAndClearDataForEndSuccess(@Param("id") String theChunkId, @Param("et") Date theEndTime, @Param("rp") int theRecordsProcessed, @Param("status") StatusEnum theInProgress);

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

@@ -1,39 +0,0 @@
-package ca.uhn.fhir.jpa.dao.data;
-
-import ca.uhn.fhir.jpa.entity.BulkExportCollectionEntity;
-import org.springframework.data.jpa.repository.JpaRepository;
-import org.springframework.data.jpa.repository.Modifying;
-import org.springframework.data.jpa.repository.Query;
-import org.springframework.data.repository.query.Param;
-
-/*
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2023 Smile CDR, Inc.
- * %%
- * 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%
- */
-
-@Deprecated
-public interface IBulkExportCollectionDao extends JpaRepository<BulkExportCollectionEntity, Long>, IHapiFhirJpaRepository {
-
-	@Modifying
-	@Query("DELETE FROM BulkExportCollectionEntity t")
-	void deleteAllFiles();
-
-	@Modifying
-	@Query("DELETE FROM BulkExportCollectionEntity t WHERE t.myId = :pid")
-	void deleteByPid(@Param("pid") Long theId);
-}

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

@@ -1,39 +0,0 @@
-package ca.uhn.fhir.jpa.dao.data;
-
-import ca.uhn.fhir.jpa.entity.BulkExportCollectionFileEntity;
-import org.springframework.data.jpa.repository.JpaRepository;
-import org.springframework.data.jpa.repository.Modifying;
-import org.springframework.data.jpa.repository.Query;
-import org.springframework.data.repository.query.Param;
-
-/*
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2023 Smile CDR, Inc.
- * %%
- * 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%
- */
-
-public interface IBulkExportCollectionFileDao extends JpaRepository<BulkExportCollectionFileEntity, Long>, IHapiFhirJpaRepository {
-
-	@Modifying
-	@Query("DELETE FROM BulkExportCollectionFileEntity t")
-	void deleteAllFiles();
-
-	@Modifying
-	@Query("DELETE FROM BulkExportCollectionFileEntity t WHERE t.myId = :pid")
-	void deleteByPid(@Param("pid") Long theId);
-
-}

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

@@ -34,25 +34,6 @@ import java.util.Optional;
 
 public interface IBulkExportJobDao extends JpaRepository<BulkExportJobEntity, Long>, IHapiFhirJpaRepository {
 
-	@Query("SELECT j FROM BulkExportJobEntity j WHERE j.myJobId = :jobid")
-	Optional<BulkExportJobEntity> findByJobId(@Param("jobid") String theUuid);
-
-	@Query("SELECT j FROM BulkExportJobEntity j WHERE j.myStatus = :status")
-	Slice<BulkExportJobEntity> findByStatus(Pageable thePage, @Param("status") BulkExportJobStatusEnum theSubmitted);
-
-	@Query("SELECT j FROM BulkExportJobEntity j WHERE j.myExpiry < :cutoff")
-	Slice<BulkExportJobEntity> findByExpiry(Pageable thePage, @Param("cutoff") Date theCutoff);
-
-	@Query("SELECT j FROM BulkExportJobEntity j WHERE j.myExpiry IS NOT NULL and j.myExpiry < :cutoff AND j.myStatus <> 'BUILDING'")
-	Slice<BulkExportJobEntity> findNotRunningByExpiry(Pageable thePage, @Param("cutoff") Date theCutoff);
-
-	@Query("SELECT j FROM BulkExportJobEntity j WHERE j.myRequest = :request AND j.myCreated > :createdAfter AND j.myStatus <> :status ORDER BY j.myCreated DESC")
-	Slice<BulkExportJobEntity> findExistingJob(Pageable thePage, @Param("request") String theRequest, @Param("createdAfter") Date theCreatedAfter, @Param("status") BulkExportJobStatusEnum theNotStatus);
-
-	@Modifying
-	@Query("DELETE FROM BulkExportJobEntity t")
-	void deleteAllFiles();
-
 	@Modifying
 	@Query("DELETE FROM BulkExportJobEntity t WHERE t.myId = :pid")
 	void deleteByPid(@Param("pid") Long theId);

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

@@ -0,0 +1,74 @@
+package ca.uhn.fhir.jpa.dao.index;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2023 Smile CDR, Inc.
+ * %%
+ * 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.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+
+public class ExtractInlineReferenceParams {
+	private IBaseResource myResource;
+	private TransactionDetails myTransactionDetails;
+	private RequestDetails myRequestDetails;
+	private boolean myFailOnInvalidReferences;
+
+	public ExtractInlineReferenceParams(
+		IBaseResource theResource,
+		TransactionDetails theTransactionDetails,
+		RequestDetails theRequest
+	) {
+		myResource = theResource;
+		myTransactionDetails = theTransactionDetails;
+		myRequestDetails = theRequest;
+	}
+
+	public IBaseResource getResource() {
+		return myResource;
+	}
+
+	public void setResource(IBaseResource theResource) {
+		myResource = theResource;
+	}
+
+	public TransactionDetails getTransactionDetails() {
+		return myTransactionDetails;
+	}
+
+	public void setTransactionDetails(TransactionDetails theTransactionDetails) {
+		myTransactionDetails = theTransactionDetails;
+	}
+
+	public RequestDetails getRequestDetails() {
+		return myRequestDetails;
+	}
+
+	public void setRequestDetails(RequestDetails theRequestDetails) {
+		myRequestDetails = theRequestDetails;
+	}
+
+	public boolean isFailOnInvalidReferences() {
+		return myFailOnInvalidReferences;
+	}
+
+	public void setFailOnInvalidReferences(boolean theFailOnInvalidReferences) {
+		myFailOnInvalidReferences = theFailOnInvalidReferences;
+	}
+}

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

@@ -150,6 +150,9 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
 		assert myDontCheckActiveTransactionForUnitTest || TransactionSynchronizationManager.isSynchronizationActive();
 		assert theRequestPartitionId != null;
 
+		if (theResourceId.contains("/")) {
+			theResourceId = theResourceId.substring(theResourceId.indexOf("/") + 1);
+		}
 		IdDt id = new IdDt(theResourceType, theResourceId);
 		Map<String, List<IResourceLookup<JpaPid>>> matches = translateForcedIdToPids(theRequestPartitionId,
 			Collections.singletonList(id),

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

@@ -113,7 +113,9 @@ public class SearchParamWithInlineReferencesExtractor {
 	}
 
 	public void populateFromResource(RequestPartitionId theRequestPartitionId, ResourceIndexedSearchParams theParams, TransactionDetails theTransactionDetails, ResourceTable theEntity, IBaseResource theResource, ResourceIndexedSearchParams theExistingParams, RequestDetails theRequest, boolean theFailOnInvalidReference) {
-		extractInlineReferences(theResource, theTransactionDetails, theRequest);
+		ExtractInlineReferenceParams theExtractParams = new ExtractInlineReferenceParams(theResource, theTransactionDetails, theRequest);
+		theExtractParams.setFailOnInvalidReferences(theFailOnInvalidReference);
+		extractInlineReferences(theExtractParams);
 
 		mySearchParamExtractorService.extractFromResource(theRequestPartitionId, theRequest, theParams, theExistingParams, theEntity, theResource, theTransactionDetails, theFailOnInvalidReference);
 
@@ -188,16 +190,32 @@ public class SearchParamWithInlineReferencesExtractor {
 		myContext = theContext;
 	}
 
+	@Deprecated
+	public void extractInlineReferences(
+		IBaseResource theResource,
+		TransactionDetails theTransactionDetails,
+		RequestDetails theRequest
+	) {
+		extractInlineReferences(new ExtractInlineReferenceParams(theResource, theTransactionDetails, theRequest));
+	}
+
 	/**
-	 * Handle references within the resource that are match URLs, for example references like "Patient?identifier=foo". These match URLs are resolved and replaced with the ID of the
+	 * Handle references within the resource that are match URLs, for example references like "Patient?identifier=foo".
+	 * These match URLs are resolved and replaced with the ID of the
 	 * matching resource.
+	 *
+	 * This method is *only* called from UPDATE path
 	 */
-	public void extractInlineReferences(IBaseResource theResource, TransactionDetails theTransactionDetails, RequestDetails theRequest) {
+	public void extractInlineReferences(ExtractInlineReferenceParams theParams) {
 		if (!myDaoConfig.isAllowInlineMatchUrlReferences()) {
 			return;
 		}
+		IBaseResource resource = theParams.getResource();
+		RequestDetails theRequest = theParams.getRequestDetails();
+		TransactionDetails theTransactionDetails = theParams.getTransactionDetails();
+
 		FhirTerser terser = myContext.newTerser();
-		List<IBaseReference> allRefs = terser.getAllPopulatedChildElementsOfType(theResource, IBaseReference.class);
+		List<IBaseReference> allRefs = terser.getAllPopulatedChildElementsOfType(resource, IBaseReference.class);
 		for (IBaseReference nextRef : allRefs) {
 			IIdType nextId = nextRef.getReferenceElement();
 			String nextIdText = nextId.getValue();
@@ -229,7 +247,6 @@ public class SearchParamWithInlineReferencesExtractor {
 
 				JpaPid match;
 				if (matches.isEmpty()) {
-
 					Optional<IBasePersistedResource> placeholderOpt = myDaoResourceLinkResolver.createPlaceholderTargetIfConfiguredToDoSo(matchResourceType, nextRef, null, theRequest, theTransactionDetails);
 					if (placeholderOpt.isPresent()) {
 						match = (JpaPid) placeholderOpt.get().getPersistentId();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java

@@ -88,8 +88,24 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 		init620();
 		init630();
 		init640();
+		init660();
 	}
 
+	protected void init660() {
+
+
+		Builder version = forVersion(VersionEnum.V6_6_0);
+		// fix Postgres clob types - that stupid oid driver problem is still there
+		// BT2_JOB_INSTANCE.PARAMS_JSON_LOB
+		version.onTable("BT2_JOB_INSTANCE")
+			.migratePostgresTextClobToBinaryClob("20230208.1", "PARAMS_JSON_LOB");
+		// BT2_JOB_INSTANCE.REPORT
+		version.onTable("BT2_JOB_INSTANCE")
+			.migratePostgresTextClobToBinaryClob("20230208.2", "REPORT");
+		// BT2_WORK_CHUNK.CHUNK_DATA
+		version.onTable("BT2_WORK_CHUNK")
+			.migratePostgresTextClobToBinaryClob("20230208.3", "CHUNK_DATA");
+	}
 	protected void init640() {
 
 	}
@@ -113,17 +129,7 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 			.online(true)
 			.withColumns("SEARCH_PID")
 			.onlyAppliesToPlatforms(NON_AUTOMATIC_FK_INDEX_PLATFORMS);
-
+;
-		// fix Postgres clob types - that stupid oid driver problem is still there
-		// BT2_JOB_INSTANCE.PARAMS_JSON_LOB
-		version.onTable("BT2_JOB_INSTANCE")
-			.migratePostgresTextClobToBinaryClob("20230208.1", "PARAMS_JSON_LOB");
-		// BT2_JOB_INSTANCE.REPORT
-		version.onTable("BT2_JOB_INSTANCE")
-			.migratePostgresTextClobToBinaryClob("20230208.2", "REPORT");
-		// BT2_WORK_CHUNK.CHUNK_DATA
-		version.onTable("BT2_WORK_CHUNK")
-			.migratePostgresTextClobToBinaryClob("20230208.3", "CHUNK_DATA");
 
 	}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/Batch2DaoSvcImpl.java

@@ -51,6 +51,7 @@ import javax.annotation.Nullable;
 import java.util.Date;
 import java.util.List;
 import java.util.stream.Collectors;
+import static org.apache.commons.collections4.CollectionUtils.isNotEmpty;
 
 public class Batch2DaoSvcImpl implements IBatch2DaoSvc {
 
@@ -99,8 +100,9 @@ public class Batch2DaoSvcImpl implements IBatch2DaoSvc {
 		List<IResourcePersistentId> ids = dao.searchForIds(searchParamMap, request);
 
 		Date lastDate = null;
-		if (ids.size() > 0) {
+		if (isNotEmpty(ids)) {
-			lastDate = dao.readByPid(ids.get(ids.size() - 1)).getMeta().getLastUpdated();
+			IResourcePersistentId lastResourcePersistentId = ids.get(ids.size() - 1);
+			lastDate = dao.readByPid(lastResourcePersistentId, true).getMeta().getLastUpdated();
 		}
 
 		return new HomogeneousResourcePidList(resourceType, ids, lastDate);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/export/svc/BulkDataExportJobSchedulingHelperImplTest.java

@@ -0,0 +1,382 @@
+package ca.uhn.fhir.jpa.bulk.export.svc;
+
+import ca.uhn.fhir.batch2.api.IJobPersistence;
+import ca.uhn.fhir.batch2.model.JobInstance;
+import ca.uhn.fhir.batch2.model.StatusEnum;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.api.model.BulkExportJobResults;
+import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
+import ca.uhn.fhir.util.Batch2JobDefinitionConstants;
+import ca.uhn.fhir.util.JsonUtil;
+import org.apache.commons.lang3.time.DateUtils;
+import org.hl7.fhir.instance.model.api.IBaseBinary;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.Binary;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.ArgumentCaptor;
+import org.mockito.Captor;
+import org.mockito.Mock;
+import org.mockito.junit.jupiter.MockitoExtension;
+import org.mockito.stubbing.Answer;
+import org.mockito.stubbing.OngoingStubbing;
+import org.springframework.data.domain.PageRequest;
+import org.springframework.data.util.Pair;
+import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.support.TransactionCallback;
+import org.springframework.transaction.support.TransactionTemplate;
+
+import javax.annotation.Nonnull;
+import java.time.LocalDateTime;
+import java.time.ZoneId;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
+import java.util.stream.IntStream;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.ArgumentMatchers.eq;
+import static org.mockito.Mockito.never;
+import static org.mockito.Mockito.verify;
+import static org.mockito.Mockito.when;
+
+@ExtendWith(MockitoExtension.class)
+public class BulkDataExportJobSchedulingHelperImplTest {
+	@Mock
+	private DaoConfig myDaoConfig;
+
+	@Mock
+	private PlatformTransactionManager myTxManager;
+
+	@Mock
+	private TransactionTemplate myTxTemplate;
+
+	@Mock
+	private IJobPersistence myJpaJobPersistence;
+
+	@Mock
+	private BulkExportHelperService myBulkExportHelperSvc;
+
+	@Mock
+	private DaoRegistry myDaoRegistry;
+
+	@Mock
+	private IFhirResourceDao<IBaseBinary> myBinaryDao;
+
+	@Captor
+	private ArgumentCaptor<Date> myCutoffCaptor;
+
+	private BulkDataExportJobSchedulingHelperImpl myBulkDataExportJobSchedulingHelper;
+	private final FhirContext myFhirContext = FhirContext.forR4Cached();
+
+	@Test
+	public void testPurgeExpiredFilesDisabledDoesNothing() {
+		setupTestDisabled();
+
+		myBulkDataExportJobSchedulingHelper.purgeExpiredFiles();
+
+		verify(myJpaJobPersistence, never()).fetchInstance(anyString());
+		verify(myBulkExportHelperSvc, never()).toId(anyString());
+		verify(myJpaJobPersistence, never()).deleteInstanceAndChunks(anyString());
+	}
+
+	@Test
+	public void purgeExpiredFilesNothingToDeleteOneHourRetention() {
+		final int expectedRetentionHours = 1;
+
+		setupTestEnabled(expectedRetentionHours, List.of());
+
+		myBulkDataExportJobSchedulingHelper.purgeExpiredFiles();
+
+
+		verify(myJpaJobPersistence, never()).fetchInstance(anyString());
+		verify(myBulkExportHelperSvc, never()).toId(anyString());
+		verify(myBinaryDao, never()).delete(any(IIdType.class), any(SystemRequestDetails.class));
+		verify(myJpaJobPersistence, never()).deleteInstanceAndChunks(anyString());
+
+		final Date cutoffDate = myCutoffCaptor.getValue();
+		assertEquals(DateUtils.truncate(computeDateFromConfig(expectedRetentionHours), Calendar.SECOND), DateUtils.truncate(cutoffDate, Calendar.SECOND));
+	}
+
+	@Test
+	public void purgeExpiredFilesSingleJobSingleBinaryOneHourRetention_NULL_reportString() {
+		final int expectedRetentionHours = 1;
+		final int numBinariesPerJob = 1;
+		final List<JobInstance> jobInstances = getJobInstances(numBinariesPerJob, StatusEnum.COMPLETED);
+
+		jobInstances.get(0).setReport(null);
+
+		setupTestEnabledNoBinaries(expectedRetentionHours, jobInstances);
+
+		myBulkDataExportJobSchedulingHelper.purgeExpiredFiles();
+
+		for (JobInstance jobInstance : jobInstances) {
+			verify(myJpaJobPersistence).fetchInstance(jobInstance.getInstanceId());
+			verify(myBulkExportHelperSvc, never()).toId(anyString());
+			verify(myBinaryDao, never()).delete(any(IIdType.class), any(SystemRequestDetails.class));
+			verify(myJpaJobPersistence).deleteInstanceAndChunks(jobInstance.getInstanceId());
+		}
+
+		final Date cutoffDate = myCutoffCaptor.getValue();
+		assertEquals(DateUtils.truncate(computeDateFromConfig(expectedRetentionHours), Calendar.MINUTE), DateUtils.truncate(cutoffDate, Calendar.MINUTE));
+	}
+
+	@Test
+	public void purgeExpiredFilesSingleJobSingleBinaryOneHourRetention_BAD_reportString() {
+		final int expectedRetentionHours = 1;
+		final int numBinariesPerJob = 1;
+		final List<JobInstance> jobInstances = getJobInstances(numBinariesPerJob, StatusEnum.COMPLETED);
+
+		jobInstances.get(0).setReport("{garbage}");
+
+		setupTestEnabledNoBinaries(expectedRetentionHours, jobInstances);
+
+		myBulkDataExportJobSchedulingHelper.purgeExpiredFiles();
+
+		for (JobInstance jobInstance : jobInstances) {
+			verify(myJpaJobPersistence).fetchInstance(jobInstance.getInstanceId());
+			verify(myBulkExportHelperSvc, never()).toId(anyString());
+			verify(myBinaryDao, never()).delete(any(IIdType.class), any(SystemRequestDetails.class));
+			verify(myJpaJobPersistence).deleteInstanceAndChunks(jobInstance.getInstanceId());
+		}
+
+		final Date cutoffDate = myCutoffCaptor.getValue();
+		assertEquals(DateUtils.truncate(computeDateFromConfig(expectedRetentionHours), Calendar.MINUTE), DateUtils.truncate(cutoffDate, Calendar.MINUTE));
+	}
+
+	@Test
+	public void purgeExpiredFilesSingleJobSingleBinaryOneHourRetention() {
+		final int expectedRetentionHours = 1;
+		final int numBinariesPerJob = 1;
+		final List<JobInstance> jobInstances = getJobInstances(numBinariesPerJob, StatusEnum.COMPLETED);
+
+		setupTestEnabled(expectedRetentionHours, jobInstances);
+
+		myBulkDataExportJobSchedulingHelper.purgeExpiredFiles();
+
+		for (JobInstance jobInstance : jobInstances) {
+			verify(myJpaJobPersistence).fetchInstance(jobInstance.getInstanceId());
+			for (int index = 0; index < numBinariesPerJob; index++) {
+				verify(myBulkExportHelperSvc).toId(jobInstance.getInstanceId() + "-binary-" + index);
+				verify(myBinaryDao).delete(eq(toId(jobInstance.getInstanceId() + "-binary-" + index)), any(SystemRequestDetails.class));
+			}
+			verify(myJpaJobPersistence).deleteInstanceAndChunks(jobInstance.getInstanceId());
+		}
+
+		final Date cutoffDate = myCutoffCaptor.getValue();
+		assertEquals(DateUtils.truncate(computeDateFromConfig(expectedRetentionHours), Calendar.MINUTE), DateUtils.truncate(cutoffDate, Calendar.MINUTE));
+	}
+
+	@Test
+	public void purgeExpiredFilesSingleJobSingleBinaryOneHourRetentionStatusFailed() {
+		final int expectedRetentionHours = 1;
+		final int numBinariesPerJob = 1;
+		final List<JobInstance> jobInstances = getJobInstances(numBinariesPerJob, StatusEnum.COMPLETED);
+
+		setupTestEnabled(expectedRetentionHours, jobInstances);
+
+		myBulkDataExportJobSchedulingHelper.purgeExpiredFiles();
+
+		for (JobInstance jobInstance : jobInstances) {
+			verify(myJpaJobPersistence).fetchInstance(jobInstance.getInstanceId());
+			for (int index = 0; index < numBinariesPerJob; index++) {
+				verify(myBulkExportHelperSvc).toId(jobInstance.getInstanceId() + "-binary-" + index);
+				verify(myBinaryDao).delete(eq(toId(jobInstance.getInstanceId() + "-binary-" + index)), any(SystemRequestDetails.class));
+			}
+			verify(myJpaJobPersistence).deleteInstanceAndChunks(jobInstance.getInstanceId());
+		}
+
+		final Date cutoffDate = myCutoffCaptor.getValue();
+		assertEquals(DateUtils.truncate(computeDateFromConfig(expectedRetentionHours), Calendar.MINUTE), DateUtils.truncate(cutoffDate, Calendar.MINUTE));
+	}
+
+	@Test
+	public void purgeExpiredFilesSingleJobSingleBinaryTwoHourRetention() {
+		final int expectedRetentionHours = 2;
+		final int numBinariesPerJob = 1;
+		final List<JobInstance> jobInstances = getJobInstances(numBinariesPerJob, StatusEnum.COMPLETED);
+
+		setupTestEnabled(expectedRetentionHours, jobInstances);
+
+		myBulkDataExportJobSchedulingHelper.purgeExpiredFiles();
+
+		for (JobInstance jobInstance : jobInstances) {
+			verify(myJpaJobPersistence).fetchInstance(jobInstance.getInstanceId());
+			for (int index = 0; index < numBinariesPerJob; index++) {
+				verify(myBulkExportHelperSvc).toId(jobInstance.getInstanceId() + "-binary-" + index);
+				verify(myBinaryDao).delete(eq(toId(jobInstance.getInstanceId() + "-binary-" + index)), any(SystemRequestDetails.class));
+			}
+			verify(myJpaJobPersistence).deleteInstanceAndChunks(jobInstance.getInstanceId());
+		}
+
+		final Date cutoffDate = myCutoffCaptor.getValue();
+
+		assertEquals(DateUtils.truncate(computeDateFromConfig(expectedRetentionHours), Calendar.MINUTE), DateUtils.truncate(cutoffDate, Calendar.MINUTE));
+	}
+
+	@Test
+	public void purgeExpiredFilesMultipleJobsMultipleBinariesTwoHourRetention() {
+		final int expectedRetentionHours = 2;
+		final int numBinariesPerJob = 3;
+		final List<JobInstance> jobInstances = getJobInstances( numBinariesPerJob, StatusEnum.COMPLETED, StatusEnum.COMPLETED, StatusEnum.COMPLETED);
+
+		setupTestEnabled(expectedRetentionHours, jobInstances);
+
+		myBulkDataExportJobSchedulingHelper.purgeExpiredFiles();
+
+		for (JobInstance jobInstance : jobInstances) {
+			verify(myJpaJobPersistence).fetchInstance(jobInstance.getInstanceId());
+			for (int index = 0; index < numBinariesPerJob; index++) {
+				verify(myBulkExportHelperSvc).toId(jobInstance.getInstanceId() + "-binary-" + index);
+				verify(myBinaryDao).delete(eq(toId(jobInstance.getInstanceId() + "-binary-" + index)), any(SystemRequestDetails.class));
+			}
+			verify(myJpaJobPersistence).deleteInstanceAndChunks(jobInstance.getInstanceId());
+		}
+
+		final Date cutoffDate = myCutoffCaptor.getValue();
+
+		assertEquals(DateUtils.truncate(computeDateFromConfig(expectedRetentionHours), Calendar.MINUTE), DateUtils.truncate(cutoffDate, Calendar.MINUTE));
+	}
+
+	@Test
+	public void purgeExpiredFilesMultipleJobsMultipleBinariesTwoHourRetentionMixedStatuses() {
+		final int expectedRetentionHours = 2;
+		final int numBinariesPerJob = 3;
+		final List<JobInstance> jobInstances = getJobInstances( numBinariesPerJob, StatusEnum.COMPLETED, StatusEnum.FAILED, StatusEnum.COMPLETED);
+
+		setupTestEnabled(expectedRetentionHours, jobInstances);
+
+		myBulkDataExportJobSchedulingHelper.purgeExpiredFiles();
+
+		for (JobInstance jobInstance : jobInstances) {
+			verify(myJpaJobPersistence).fetchInstance(jobInstance.getInstanceId());
+			if (StatusEnum.FAILED != jobInstance.getStatus()) {
+				for (int index = 0; index < numBinariesPerJob; index++) {
+					verify(myBulkExportHelperSvc).toId(jobInstance.getInstanceId() + "-binary-" + index);
+					verify(myBinaryDao).delete(eq(toId(jobInstance.getInstanceId() + "-binary-" + index)), any(SystemRequestDetails.class));
+				}
+
+				verify(myJpaJobPersistence).deleteInstanceAndChunks(jobInstance.getInstanceId());
+			}
+		}
+
+		final Date cutoffDate = myCutoffCaptor.getValue();
+
+		assertEquals(DateUtils.truncate(computeDateFromConfig(expectedRetentionHours), Calendar.MINUTE), DateUtils.truncate(cutoffDate, Calendar.MINUTE));
+	}
+
+	@Nonnull
+	private static List<JobInstance> getJobInstances(int theNumBinaries, StatusEnum... theStatusEnums) {
+		return IntStream.range(0, theStatusEnums.length)
+			.mapToObj(index -> Pair.of(index, theStatusEnums[index]))
+			.map(pair -> {
+				final JobInstance jobInstance = new JobInstance();
+				final StatusEnum status = pair.getSecond();
+				final String instanceId = status.name() + pair.getFirst();
+				jobInstance.setInstanceId(instanceId);
+				jobInstance.setReport(serialize(getBulkExportJobResults(instanceId, theNumBinaries)));
+				jobInstance.setStatus(status);
+				return jobInstance;
+		}).toList();
+	}
+
+	private static String serialize(BulkExportJobResults theBulkExportJobResults) {
+		return JsonUtil.serialize(theBulkExportJobResults);
+	}
+
+	@Nonnull
+	private static BulkExportJobResults getBulkExportJobResults(String theInstanceId, int theNumBinaries) {
+		final BulkExportJobResults bulkExportJobResults = new BulkExportJobResults();
+		bulkExportJobResults.setResourceTypeToBinaryIds(Map.of("Patient",
+			IntStream.range(0, theNumBinaries)
+				.mapToObj(theInt -> theInstanceId + "-binary-" + theInt)
+				.toList()));
+		return bulkExportJobResults;
+	}
+
+	@Nonnull
+	private Date computeDateFromConfig(int theExpectedRetentionHours) {
+		return Date.from(LocalDateTime.now()
+			.minusHours(theExpectedRetentionHours)
+			.atZone(ZoneId.systemDefault())
+			.toInstant());
+	}
+
+	private void setupTestDisabled() {
+		setupTest(false, -1, List.of(), false);
+	}
+
+	private void setupTestEnabled(int theRetentionHours, List<JobInstance> theJobInstances) {
+		setupTest(true, theRetentionHours, theJobInstances, true);
+	}
+
+	private void setupTestEnabledNoBinaries(int theRetentionHours, List<JobInstance> theJobInstances) {
+		setupTest(true, theRetentionHours, theJobInstances, false);
+	}
+
+	private void setupTest(boolean theIsEnabled, int theRetentionHours, List<JobInstance> theJobInstances, boolean theIsEnableBinaryMocks) {
+		myBulkDataExportJobSchedulingHelper = new BulkDataExportJobSchedulingHelperImpl(myDaoRegistry, myTxManager, myDaoConfig, myBulkExportHelperSvc, myJpaJobPersistence, myTxTemplate);
+
+		when(myDaoConfig.isEnableTaskBulkExportJobExecution()).thenReturn(theIsEnabled);
+
+		if (!theIsEnabled) {
+			return;
+		}
+
+
+		final Answer<List<JobInstance>> fetchInstancesAnswer = theInvocationOnMock -> {
+			final TransactionCallback<List<JobInstance>> transactionCallback = theInvocationOnMock.getArgument(0);
+			return transactionCallback.doInTransaction(null);
+		};
+
+		final Answer<Void> purgeExpiredJobsAnswer = theInvocationOnMock -> {
+			final TransactionCallback<Optional<JobInstance>> transactionCallback = theInvocationOnMock.getArgument(0);
+			transactionCallback.doInTransaction(null);
+			return null;
+		};
+
+		when(myJpaJobPersistence.fetchInstances(eq(Batch2JobDefinitionConstants.BULK_EXPORT),
+			eq(StatusEnum.getEndedStatuses()),
+			myCutoffCaptor.capture(),
+			any(PageRequest.class)))
+				.thenReturn(theJobInstances);
+
+		when(myTxTemplate.execute(any()))
+			.thenAnswer(fetchInstancesAnswer).thenAnswer(purgeExpiredJobsAnswer);
+
+		when(myDaoConfig.getBulkExportFileRetentionPeriodHours())
+			.thenReturn(theRetentionHours);
+
+		if (theJobInstances.isEmpty()) {
+			return;
+		}
+
+		OngoingStubbing<Optional<JobInstance>> when = when(myJpaJobPersistence.fetchInstance(anyString()));
+
+		for (JobInstance jobInstance : theJobInstances) {
+			when = when.thenReturn(Optional.of(jobInstance));
+		}
+
+		if (!theIsEnableBinaryMocks) {
+			return;
+		}
+
+		when(myBulkExportHelperSvc.toId(anyString()))
+			.thenAnswer(theInvocationOnMock -> toId(theInvocationOnMock.getArgument(0)));
+
+		when(myDaoRegistry.getResourceDao(Binary.class.getSimpleName())).thenReturn(myBinaryDao);
+	}
+
+	private IIdType toId(String theResourceId) {
+		final IIdType retVal = myFhirContext.getVersion().newIdType();
+		retVal.setValue(theResourceId);
+		return retVal;
+	}
+}

hapi-fhir-jpaserver-elastic-test-utilities/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-ips/pom.xml

@@ -3,7 +3,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-mdm/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/dao/MdmLinkDaoSvc.java

@@ -73,11 +73,9 @@ public class MdmLinkDaoSvc<P extends IResourcePersistentId, M extends IMdmLink<P
 		mdmLink.setEidMatch(theMatchOutcome.isEidMatch() | mdmLink.isEidMatchPresent());
 		mdmLink.setHadToCreateNewGoldenResource(theMatchOutcome.isCreatedNewResource() | mdmLink.getHadToCreateNewGoldenResource());
 		mdmLink.setMdmSourceType(myFhirContext.getResourceType(theSourceResource));
-		if (mdmLink.getScore() != null) {
+
-			mdmLink.setScore(Math.max(theMatchOutcome.score, mdmLink.getScore()));
+		setScoreProperties(theMatchOutcome, mdmLink);
-		} else {
+
-			mdmLink.setScore(theMatchOutcome.score);
-		}
 		// Add partition for the mdm link if it's available in the source resource
 		RequestPartitionId partitionId = (RequestPartitionId) theSourceResource.getUserData(Constants.RESOURCE_PARTITION_ID);
 		if (partitionId != null && partitionId.getFirstPartitionIdOrNull() != null) {
@@ -91,6 +89,24 @@ public class MdmLinkDaoSvc<P extends IResourcePersistentId, M extends IMdmLink<P
 		return mdmLink;
 	}
 
+	private void setScoreProperties(MdmMatchOutcome theMatchOutcome, M mdmLink) {
+		if (theMatchOutcome.getScore() != null) {
+			mdmLink.setScore(  mdmLink.getScore() != null
+				? Math.max(theMatchOutcome.getNormalizedScore(), mdmLink.getScore())
+				: theMatchOutcome.getNormalizedScore() );
+		}
+
+		if (theMatchOutcome.getVector() != null) {
+			mdmLink.setVector( mdmLink.getVector() != null
+				? Math.max(theMatchOutcome.getVector(), mdmLink.getVector())
+				: theMatchOutcome.getVector() );
+		}
+
+		mdmLink.setRuleCount( mdmLink.getRuleCount() != null
+			? Math.max(theMatchOutcome.getMdmRuleCount(), mdmLink.getRuleCount())
+			: theMatchOutcome.getMdmRuleCount() );
+	}
+
 	@Nonnull
 	public M getOrCreateMdmLinkByGoldenResourceAndSourceResource(
 		IAnyResource theGoldenResource, IAnyResource theSourceResource
@@ -127,7 +143,6 @@ public class MdmLinkDaoSvc<P extends IResourcePersistentId, M extends IMdmLink<P
 	 * @param theSourceResourcePid The ResourcepersistenceId of the Source resource
 	 * @return The {@link IMdmLink} entity that matches these criteria if exists
 	 */
-	@SuppressWarnings("unchecked")
 	public Optional<M> getLinkByGoldenResourcePidAndSourceResourcePid(P theGoldenResourcePid, P theSourceResourcePid) {
 		if (theSourceResourcePid == null || theGoldenResourcePid == null) {
 			return Optional.empty();

hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchLinkSvc.java

@@ -94,7 +94,7 @@ public class MdmMatchLinkSvc {
 
 	private void handleMdmWithMultipleCandidates(IAnyResource theResource, CandidateList theCandidateList, MdmTransactionContext theMdmTransactionContext) {
 		MatchedGoldenResourceCandidate firstMatch = theCandidateList.getFirstMatch();
-		IResourcePersistentId sampleGoldenResourcePid = firstMatch.getCandidateGoldenResourcePid();
+		IResourcePersistentId<?> sampleGoldenResourcePid = firstMatch.getCandidateGoldenResourcePid();
 		boolean allSameGoldenResource = theCandidateList.stream()
 			.allMatch(candidate -> candidate.getCandidateGoldenResourcePid().equals(sampleGoldenResourcePid));
 
@@ -105,17 +105,7 @@ public class MdmMatchLinkSvc {
 			log(theMdmTransactionContext, "MDM received multiple match candidates, that were linked to different Golden Resources. Setting POSSIBLE_DUPLICATES and POSSIBLE_MATCHES.");
 
 			//Set them all as POSSIBLE_MATCH
-			List<IAnyResource> goldenResources = new ArrayList<>();
+			List<IAnyResource> goldenResources = createPossibleMatches(theResource, theCandidateList, theMdmTransactionContext);
-			for (MatchedGoldenResourceCandidate matchedGoldenResourceCandidate : theCandidateList.getCandidates()) {
-				IAnyResource goldenResource = myMdmGoldenResourceFindingSvc
-					.getGoldenResourceFromMatchedGoldenResourceCandidate(matchedGoldenResourceCandidate, theMdmTransactionContext.getResourceType());
-				MdmMatchOutcome outcome = new MdmMatchOutcome(matchedGoldenResourceCandidate.getMatchResult().vector,
-					matchedGoldenResourceCandidate.getMatchResult().getNormalizedScore());
-				outcome.setMatchResultEnum(MdmMatchResultEnum.POSSIBLE_MATCH);
-				outcome.setEidMatch(theCandidateList.isEidMatch());
-				myMdmLinkSvc.updateLink(goldenResource, theResource, outcome, MdmLinkSourceEnum.AUTO, theMdmTransactionContext);
-				goldenResources.add(goldenResource);
-			}
 
 			//Set all GoldenResources as POSSIBLE_DUPLICATE of the last GoldenResource.
 			IAnyResource firstGoldenResource = goldenResources.get(0);
@@ -129,6 +119,26 @@ public class MdmMatchLinkSvc {
 		}
 	}
 
+	private List<IAnyResource> createPossibleMatches(IAnyResource theResource, CandidateList theCandidateList, MdmTransactionContext theMdmTransactionContext) {
+		List<IAnyResource> goldenResources = new ArrayList<>();
+
+		for (MatchedGoldenResourceCandidate matchedGoldenResourceCandidate : theCandidateList.getCandidates()) {
+			IAnyResource goldenResource = myMdmGoldenResourceFindingSvc
+				.getGoldenResourceFromMatchedGoldenResourceCandidate(matchedGoldenResourceCandidate, theMdmTransactionContext.getResourceType());
+
+			MdmMatchOutcome outcome = new MdmMatchOutcome(matchedGoldenResourceCandidate.getMatchResult().getVector(),
+					matchedGoldenResourceCandidate.getMatchResult().getScore())
+				.setMdmRuleCount( matchedGoldenResourceCandidate.getMatchResult().getMdmRuleCount());
+
+			outcome.setMatchResultEnum(MdmMatchResultEnum.POSSIBLE_MATCH);
+			outcome.setEidMatch(theCandidateList.isEidMatch());
+			myMdmLinkSvc.updateLink(goldenResource, theResource, outcome, MdmLinkSourceEnum.AUTO, theMdmTransactionContext);
+			goldenResources.add(goldenResource);
+		}
+
+		return goldenResources;
+	}
+
 	private void handleMdmWithNoCandidates(IAnyResource theResource, MdmTransactionContext theMdmTransactionContext) {
 		log(theMdmTransactionContext, String.format("There were no matched candidates for MDM, creating a new %s Golden Resource.", theResource.getIdElement().getResourceType()));
 		IAnyResource newGoldenResource = myGoldenResourceHelper.createGoldenResourceFromMdmSourceResource(theResource, theMdmTransactionContext);

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/BaseMdmR4Test.java

@@ -569,6 +569,10 @@ abstract public class BaseMdmR4Test extends BaseJpaR4Test {
 		assertFields(MdmLink::getEidMatch, theExpectedValues);
 	}
 
+	protected void assertLinksMatchScore(Double... theExpectedValues) {
+		assertFields(MdmLink::getScore, theExpectedValues);
+	}
+
 	public SearchParameterMap buildGoldenResourceSearchParameterMap() {
 		SearchParameterMap spMap = new SearchParameterMap();
 		spMap.setLoadSynchronous(true);

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/dao/MdmLinkDaoSvcTest.java

@@ -100,7 +100,6 @@ public class MdmLinkDaoSvcTest extends BaseMdmR4Test {
 		mdmLink.setUpdated(new Date());
 		mdmLink.setGoldenResourcePersistenceId(JpaPid.fromId(thePatientPid));
 		mdmLink.setSourcePersistenceId(runInTransaction(()->myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), patient)));
-		MdmLink saved= myMdmLinkDao.save(mdmLink);
+		return myMdmLinkDao.save(mdmLink);
-		return saved;
 	}
 }

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/provider/MdmProviderQueryLinkR4Test.java

@@ -10,6 +10,7 @@ import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import ca.uhn.fhir.test.utilities.RangeTestHelper;
 import ca.uhn.fhir.util.ParametersUtil;
 import ca.uhn.fhir.util.StopWatch;
 import org.apache.commons.lang3.StringUtils;
@@ -76,9 +77,12 @@ public class MdmProviderQueryLinkR4Test extends BaseLinkR4Test {
 		JpaPid sourcePatient2Pid = runInTransaction(()->myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), sourcePatient2));
 
 		MdmLink possibleDuplicateMdmLink = (MdmLink) myMdmLinkDaoSvc.newMdmLink();
-		possibleDuplicateMdmLink.setGoldenResourcePersistenceId(sourcePatient1Pid);
+		possibleDuplicateMdmLink.setGoldenResourcePersistenceId(sourcePatient1Pid)
-		possibleDuplicateMdmLink.setSourcePersistenceId(sourcePatient2Pid);
+			.setSourcePersistenceId(sourcePatient2Pid)
-		possibleDuplicateMdmLink.setMatchResult(MdmMatchResultEnum.POSSIBLE_DUPLICATE).setLinkSource(MdmLinkSourceEnum.AUTO);
+			.setMatchResult(MdmMatchResultEnum.POSSIBLE_DUPLICATE)
+			.setLinkSource(MdmLinkSourceEnum.AUTO)
+			.setScore(1.0)
+			.setRuleCount(1L);
 		saveLink(possibleDuplicateMdmLink);
 	}
 
@@ -89,7 +93,7 @@ public class MdmProviderQueryLinkR4Test extends BaseLinkR4Test {
 		List<Parameters.ParametersParameterComponent> list = getParametersByName(result, "link");
 		assertThat(list, hasSize(1));
 		List<Parameters.ParametersParameterComponent> part = list.get(0).getPart();
-		assertMdmLink(MDM_LINK_PROPERTY_COUNT, part, mySourcePatientId.getValue(), myPatientId.getValue(), MdmMatchResultEnum.POSSIBLE_MATCH, "false", "true", null);
+		assertMdmLink(MDM_LINK_PROPERTY_COUNT, part, mySourcePatientId.getValue(), myPatientId.getValue(), MdmMatchResultEnum.POSSIBLE_MATCH, "false", "true", "1");
 	}
 
 	@Test
@@ -99,7 +103,7 @@ public class MdmProviderQueryLinkR4Test extends BaseLinkR4Test {
 		List<Parameters.ParametersParameterComponent> list = getParametersByName(result, "link");
 		assertThat("All resources with Patient type found", list, hasSize(3));
 		List<Parameters.ParametersParameterComponent> part = list.get(0).getPart();
-		assertMdmLink(MDM_LINK_PROPERTY_COUNT, part, mySourcePatientId.getValue(), myPatientId.getValue(), MdmMatchResultEnum.POSSIBLE_MATCH, "false", "true", null);
+		assertMdmLink(MDM_LINK_PROPERTY_COUNT, part, mySourcePatientId.getValue(), myPatientId.getValue(), MdmMatchResultEnum.POSSIBLE_MATCH, "false", "true", "1");
 	}
 
 
@@ -377,7 +381,7 @@ public class MdmProviderQueryLinkR4Test extends BaseLinkR4Test {
 		List<Parameters.ParametersParameterComponent> list = getParametersByName(result, "link");
 		assertThat(list, hasSize(4));
 		List<Parameters.ParametersParameterComponent> part = list.get(3).getPart();
-		assertMdmLink(MDM_LINK_PROPERTY_COUNT, part, goldenResourceId.getValue(), patientId.getValue(), MdmMatchResultEnum.MATCH, "false", "false", "2");
+		assertMdmLink(MDM_LINK_PROPERTY_COUNT, part, goldenResourceId.getValue(), patientId.getValue(), MdmMatchResultEnum.MATCH, "false", "false", ".666");
 	}
 
 	@Test
@@ -459,7 +463,7 @@ public class MdmProviderQueryLinkR4Test extends BaseLinkR4Test {
 			assertThat(thePart.get(5).getValue().primitiveValue(), is(theNewGoldenResource));
 
 			assertThat(thePart.get(6).getName(), is("score"));
-			assertThat(thePart.get(6).getValue().primitiveValue(), is(theScore));
+			RangeTestHelper.checkInRange(theScore, thePart.get(6).getValue().primitiveValue());
 		}
 	}
 

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkUpdaterSvcImplTest.java

@@ -16,6 +16,7 @@ import java.util.List;
 
 import static ca.uhn.fhir.mdm.api.MdmMatchResultEnum.MATCH;
 import static ca.uhn.fhir.mdm.api.MdmMatchResultEnum.NO_MATCH;
+import static ca.uhn.fhir.mdm.api.MdmMatchResultEnum.POSSIBLE_MATCH;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertNotEquals;
@@ -52,6 +53,23 @@ class MdmLinkUpdaterSvcImplTest extends BaseMdmR4Test {
 		assertLinksMatchedByEid(false, false);
 	}
 
+	@Test
+	public void testUpdateLinkPossibleMatchSavesNormalizedScore() {
+		final Patient goldenPatient = createGoldenPatient(buildJanePatient());
+		final Patient patient1 = createPatient(buildJanePatient());
+		buildUpdateLinkMdmTransactionContext();
+
+		MdmMatchOutcome matchOutcome = new MdmMatchOutcome(61L, 5.0).setMdmRuleCount(6).setMatchResultEnum(POSSIBLE_MATCH);
+		myMdmLinkDaoSvc.createOrUpdateLinkEntity(goldenPatient, patient1, matchOutcome, MdmLinkSourceEnum.MANUAL, createContextForCreate("Patient"));
+
+		final List<MdmLink> targets = myMdmLinkDaoSvc.findMdmLinksByGoldenResource(goldenPatient);
+		assertFalse(targets.isEmpty());
+		assertEquals(1, targets.size());
+		final MdmLink mdmLink = targets.get(0);
+
+		assertEquals(matchOutcome.getNormalizedScore(), mdmLink.getScore());
+	}
+
 	@Test
 	public void testUpdateLinkMatchAfterVersionChange() {
 		myMdmSettings.getMdmRules().setVersion("1");

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchLinkSvcTest.java

@@ -68,6 +68,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
 		assertLinksMatchResult(MATCH);
 		assertLinksCreatedNewResource(true);
 		assertLinksMatchedByEid(false);
+		assertLinksMatchScore(1.0);
 	}
 
 	@Test
@@ -79,6 +80,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
 		assertLinksMatchResult(MATCH);
 		assertLinksCreatedNewResource(true);
 		assertLinksMatchedByEid(false);
+		assertLinksMatchScore(1.0);
 	}
 
 	@Test
@@ -93,6 +95,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
 		assertLinksMatchResult(MATCH, MATCH);
 		assertLinksCreatedNewResource(true, true);
 		assertLinksMatchedByEid(false, false);
+		assertLinksMatchScore(1.0, 1.0);
 	}
 
 	@Test
@@ -107,6 +110,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
 		assertLinksMatchResult(MATCH, MATCH);
 		assertLinksCreatedNewResource(true, false);
 		assertLinksMatchedByEid(false, false);
+		assertLinksMatchScore(1.0, 2.0/3.0);
 	}
 
 	@Test

hapi-fhir-jpaserver-model/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-searchparam/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java

@@ -1818,10 +1818,11 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 				nextId = valueRef.getResource().getIdElement();
 			}
 
-			if (nextId == null ||
+			if (
-				nextId.isEmpty() ||
+				nextId == null ||
-				nextId.getValue().startsWith("urn:")) {
+				nextId.isEmpty()
-				// Ignore placeholder references
+			) {
+				// Ignore placeholder references that are blank
 			} else if (!theWantLocalReferences && nextId.getValue().startsWith("#")) {
 				// Ignore local refs unless we specifically want them
 			} else {

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorService.java

@@ -105,8 +105,10 @@ public class SearchParamExtractorService {
 	}
 
 	/**
-	 * This method is responsible for scanning a resource for all of the search parameter instances. I.e. for all search parameters defined for
+	 * This method is responsible for scanning a resource for all of the search parameter instances.
-	 * a given resource type, it extracts the associated indexes and populates {@literal theParams}.
+	 * I.e. for all search parameters defined for
+	 * a given resource type, it extracts the associated indexes and populates
+	 * {@literal theParams}.
 	 */
 	public void extractFromResource(RequestPartitionId theRequestPartitionId, RequestDetails theRequestDetails, ResourceIndexedSearchParams theNewParams, ResourceIndexedSearchParams theExistingParams, ResourceTable theEntity, IBaseResource theResource, TransactionDetails theTransactionDetails, boolean theFailOnInvalidReference) {
 

hapi-fhir-jpaserver-subscription/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/matcher/subscriber/SubscriptionActivatingSubscriber.java

@@ -32,6 +32,7 @@ import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedMessage;
 import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.SubscriptionUtil;
+import org.hl7.fhir.dstu2.model.Subscription;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -144,4 +145,9 @@ public class SubscriptionActivatingSubscriber extends BaseSubscriberForSubscript
 		}
 	}
 
+	public boolean isChannelTypeSupported(IBaseResource theSubscription) {
+		Subscription.SubscriptionChannelType channelType = mySubscriptionCanonicalizer.getChannelType(theSubscription).toCanonical();
+		return myDaoConfig.getSupportedSubscriptionTypes().contains(channelType);
+	}
+
 }

hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/match/registry/SubscriptionLoader.java

@@ -228,14 +228,24 @@ public class SubscriptionLoader implements IResourceChangeListener {
 	 * @return true if activated
 	 */
 	private boolean activateSubscriptionIfRequested(IBaseResource theSubscription) {
+		boolean successfullyActivated = false;
+
 		if (SubscriptionConstants.REQUESTED_STATUS.equals(mySubscriptionCanonicalizer.getSubscriptionStatus(theSubscription))) {
-			// internally, subscriptions that cannot activate will be set to error
+			if (mySubscriptionActivatingInterceptor.isChannelTypeSupported(theSubscription)) {
-			if (mySubscriptionActivatingInterceptor.activateSubscriptionIfRequired(theSubscription)) {
+				// internally, subscriptions that cannot activate will be set to error
-				return true;
+				if (mySubscriptionActivatingInterceptor.activateSubscriptionIfRequired(theSubscription)) {
+					successfullyActivated = true;
+				} else {
+					logSubscriptionNotActivatedPlusErrorIfPossible(theSubscription);
+				}
+			} else {
+				ourLog.debug("Could not activate subscription {} because channel type {} is not supported.",
+					theSubscription.getIdElement(),
+					mySubscriptionCanonicalizer.getChannelType(theSubscription));
 			}
-			logSubscriptionNotActivatedPlusErrorIfPossible(theSubscription);
 		}
-		return false;
+
+		return successfullyActivated;
 	}
 
 	/**

hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/submit/interceptor/SubscriptionValidatingInterceptor.java

@@ -83,6 +83,21 @@ public class SubscriptionValidatingInterceptor {
 		myFhirContext = theFhirContext;
 	}
 
+	// This will be deleted once the next snapshot (6.3.15) is published
+	@Deprecated
+	public void validateSubmittedSubscription(IBaseResource theSubscription) {
+		validateSubmittedSubscription(theSubscription, null, null, Pointcut.STORAGE_PRESTORAGE_RESOURCE_CREATED);
+	}
+
+	// This will be deleted once the next snapshot (6.3.15) is published
+	@Deprecated(since="6.3.14")
+	public void validateSubmittedSubscription(IBaseResource theSubscription,
+															RequestDetails theRequestDetails,
+															RequestPartitionId theRequestPartitionId) {
+
+		validateSubmittedSubscription(theSubscription, theRequestDetails, theRequestPartitionId, Pointcut.STORAGE_PRESTORAGE_RESOURCE_CREATED);
+	}
+
 	@VisibleForTesting
 	void validateSubmittedSubscription(IBaseResource theSubscription,
 												  RequestDetails theRequestDetails,

hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/match/registry/SubscriptionLoaderTest.java

@@ -134,6 +134,9 @@ public class SubscriptionLoaderTest {
 		when(mySubscriptionActivatingInterceptor.activateSubscriptionIfRequired(any(IBaseResource.class)))
 				.thenReturn(false);
 
+		when(mySubscriptionActivatingInterceptor.isChannelTypeSupported(any(IBaseResource.class)))
+			.thenReturn(true);
+
 		when(mySubscriptionCanonicalizer.getSubscriptionStatus(any())).thenReturn(SubscriptionConstants.REQUESTED_STATUS);
 		
 		// test

hapi-fhir-jpaserver-test-dstu2/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-test-dstu3/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/BaseResourceProviderDstu3Test.java

@@ -95,6 +95,7 @@ public abstract class BaseResourceProviderDstu3Test extends BaseJpaDstu3Test {
 			myPort = myServer.getPort();
 			myServerBase = myServer.getBaseUrl();
 			myClient = myServer.getFhirClient();
+			myClient.setEncoding(EncodingEnum.JSON);
 			myRestServer = myServer.getRestfulServer();
 
 			myClient.getInterceptorService().unregisterInterceptorsIf(t -> t instanceof LoggingInterceptor);

hapi-fhir-jpaserver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3Test.java

@@ -430,7 +430,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 
 		String respString = myClient.transaction().withBundle(input).prettyPrint().execute();
 		ourLog.debug(respString);
-		Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, respString);
+		Bundle bundle = myFhirContext.newJsonParser().parseResource(Bundle.class, respString);
 		IdType id = new IdType(bundle.getEntry().get(0).getResponse().getLocation());
 
 		Basic basic = myClient.read().resource(Basic.class).withId(id).execute();
@@ -1098,7 +1098,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 			//@formatter:on
 			fail();
 		} catch (PreconditionFailedException e) {
-			assertEquals("HTTP 412 Precondition Failed: " + Msg.code(962) + "Failed to DELETE resource with match URL \"Patient?identifier=testDeleteConditionalMultiple\" because this search matched 2 resources",
+			assertEquals("HTTP 412 Precondition Failed: " + Msg.code(962) + "Failed to DELETE resource with match URL \"Patient?identifier=testDeleteConditionalMultiple&_format=json\" because this search matched 2 resources",
 				e.getMessage());
 		}
 

hapi-fhir-jpaserver-test-r4/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/batch2/Batch2CoordinatorIT.java

@@ -34,6 +34,8 @@ import com.fasterxml.jackson.annotation.JsonProperty;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.ValueSource;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -45,11 +47,13 @@ import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Optional;
+import java.util.concurrent.atomic.AtomicBoolean;
 import java.util.concurrent.atomic.AtomicInteger;
 
 import static ca.uhn.fhir.batch2.config.BaseBatch2Config.CHANNEL_NAME;
 import static ca.uhn.fhir.batch2.coordinator.WorkChunkProcessor.MAX_CHUNK_ERROR_COUNT;
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.junit.jupiter.api.Assertions.fail;
@@ -216,9 +220,44 @@ public class Batch2CoordinatorIT extends BaseJpaR4Test {
 		myLastStepLatch.awaitExpected();
 	}
 
-	@Test
+	private void createThreeStepReductionJob(
-	public void testJobDefinitionWithReductionStepIT() throws InterruptedException {
+		String theJobId,
+		IJobStepWorker<TestJobParameters, VoidModel, FirstStepOutput> theFirstStep,
+		IJobStepWorker<TestJobParameters, FirstStepOutput, SecondStepOutput> theSecondStep,
+		IReductionStepWorker<TestJobParameters, SecondStepOutput, ReductionStepOutput> theReductionsStep
+	) {
+		// create job definition (it's the test method's name)
+		JobDefinition<? extends IModelJson> jd = JobDefinition.newBuilder()
+			.setJobDefinitionId(theJobId)
+			.setJobDescription("test job")
+			.setJobDefinitionVersion(TEST_JOB_VERSION)
+			.setParametersType(TestJobParameters.class)
+			.gatedExecution()
+			.addFirstStep(
+				FIRST_STEP_ID,
+				"Test first step",
+				FirstStepOutput.class,
+				theFirstStep
+			)
+			.addIntermediateStep("SECOND",
+				"Second step",
+				SecondStepOutput.class,
+				theSecondStep)
+			.addFinalReducerStep(
+				LAST_STEP_ID,
+				"Test last step",
+				ReductionStepOutput.class,
+				theReductionsStep
+			)
+			.build();
+		myJobDefinitionRegistry.addJobDefinition(jd);
+	}
+
+	@ParameterizedTest
+	@ValueSource(booleans = { true, false })
+	public void testJobDefinitionWithReductionStepIT(boolean theDelayReductionStepBool) throws InterruptedException {
 		// setup
+		String jobId = new Exception().getStackTrace()[0].getMethodName() + "_" + theDelayReductionStepBool;
 		String testInfo = "test";
 		AtomicInteger secondStepInt = new AtomicInteger();
 
@@ -235,6 +274,7 @@ public class Batch2CoordinatorIT extends BaseJpaR4Test {
 			SecondStepOutput output = new SecondStepOutput();
 			output.setValue(testInfo + secondStepInt.getAndIncrement());
 			sink.accept(output);
+
 			return RunOutcome.SUCCESS;
 		};
 
@@ -243,63 +283,66 @@ public class Batch2CoordinatorIT extends BaseJpaR4Test {
 
 			private final ArrayList<SecondStepOutput> myOutput = new ArrayList<>();
 
+			private final AtomicBoolean myBoolean = new AtomicBoolean();
+
+			private final AtomicInteger mySecondGate = new AtomicInteger();
+
 			@Override
 			public ChunkOutcome consume(ChunkExecutionDetails<TestJobParameters, SecondStepOutput> theChunkDetails) {
 				myOutput.add(theChunkDetails.getData());
+				// 1 because we know 2 packets are coming.
+				// we'll fire the second maintenance run on the second packet
+				// which should cause multiple maintenance runs to run simultaneously
+				if (theDelayReductionStepBool && mySecondGate.getAndIncrement() == 1) {
+					ourLog.info("SECOND FORCED MAINTENANCE PASS FORCED");
+					myBatch2JobHelper.forceRunMaintenancePass();
+				}
 				return ChunkOutcome.SUCCESS();
 			}
 
 			@Nonnull
 			@Override
-			public RunOutcome run(@Nonnull StepExecutionDetails<TestJobParameters, SecondStepOutput> theStepExecutionDetails,
+			public RunOutcome run(
-										 @Nonnull IJobDataSink<ReductionStepOutput> theDataSink) throws JobExecutionFailedException {
+				@Nonnull StepExecutionDetails<TestJobParameters, SecondStepOutput> theStepExecutionDetails,
-				theDataSink.accept(new ReductionStepOutput(myOutput));
+				@Nonnull IJobDataSink<ReductionStepOutput> theDataSink
-				callLatch(myLastStepLatch, theStepExecutionDetails);
+			) throws JobExecutionFailedException {
+				boolean isRunAlready = myBoolean.getAndSet(true);
+				assertFalse(isRunAlready, "Reduction step should only be called once!");
+
+				complete(theStepExecutionDetails, theDataSink);
 				return RunOutcome.SUCCESS;
 			}
-		};
 
-		// create job definition
+			private void complete(
-		String jobId = new Exception().getStackTrace()[0].getMethodName();
+				@Nonnull StepExecutionDetails<TestJobParameters, SecondStepOutput> theStepExecutionDetails,
-		JobDefinition<? extends IModelJson> jd = JobDefinition.newBuilder()
+				@Nonnull IJobDataSink<ReductionStepOutput> theDataSink
-			.setJobDefinitionId(jobId)
+			) {
-			.setJobDescription("test job")
+				assertTrue(myBoolean.get());
-			.setJobDefinitionVersion(TEST_JOB_VERSION)
+				theDataSink.accept(new ReductionStepOutput(myOutput));
-			.setParametersType(TestJobParameters.class)
+				callLatch(myLastStepLatch, theStepExecutionDetails);
-			.gatedExecution()
+			}
-			.addFirstStep(
+		};
-				FIRST_STEP_ID,
+		createThreeStepReductionJob(jobId, first, second, last);
-				"Test first step",
-				FirstStepOutput.class,
-				first
-			)
-			.addIntermediateStep("SECOND",
-				"Second step",
-				SecondStepOutput.class,
-				second)
-			.addFinalReducerStep(
-				LAST_STEP_ID,
-				"Test last step",
-				ReductionStepOutput.class,
-				last
-			)
-			.build();
-		myJobDefinitionRegistry.addJobDefinition(jd);
 
 		// run test
 		JobInstanceStartRequest request = buildRequest(jobId);
 		myFirstStepLatch.setExpectedCount(1);
 		Batch2JobStartResponse startResponse = myJobCoordinator.startInstance(request);
+
 		String instanceId = startResponse.getJobId();
 		myFirstStepLatch.awaitExpected();
-
+		assertNotNull(instanceId);
 
 		myBatch2JobHelper.awaitGatedStepId(FIRST_STEP_ID, instanceId);
 
 		// wait for last step to finish
+		ourLog.info("Setting last step latch");
 		myLastStepLatch.setExpectedCount(1);
+
+		// waiting
 		myBatch2JobHelper.awaitJobCompletion(instanceId);
 		myLastStepLatch.awaitExpected();
+		ourLog.info("awaited the last step");
 
 		// verify
 		Optional<JobInstance> instanceOp = myJobPersistence.fetchInstance(instanceId);

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/batch2/JpaJobPersistenceImplTest.java

@@ -21,8 +21,11 @@ import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.Arguments;
 import org.junit.jupiter.params.provider.MethodSource;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.PageRequest;
 
 import javax.annotation.Nonnull;
+import java.time.LocalDateTime;
+import java.time.ZoneId;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.HashSet;
@@ -133,6 +136,86 @@ public class JpaJobPersistenceImplTest extends BaseJpaR4Test {
 		});
 	}
 
+	@Test
+	public void testFetchInstanceWithStatusAndCutoff_statues() {
+		myCaptureQueriesListener.clear();
+
+		final String completedId = storeJobInstanceAndUpdateWithEndTime(StatusEnum.COMPLETED, 1);
+		final String failedId = storeJobInstanceAndUpdateWithEndTime(StatusEnum.FAILED, 1);
+		final String erroredId = storeJobInstanceAndUpdateWithEndTime(StatusEnum.ERRORED, 1);
+		final String cancelledId = storeJobInstanceAndUpdateWithEndTime(StatusEnum.CANCELLED, 1);
+		storeJobInstanceAndUpdateWithEndTime(StatusEnum.QUEUED, 1);
+		storeJobInstanceAndUpdateWithEndTime(StatusEnum.IN_PROGRESS, 1);
+		storeJobInstanceAndUpdateWithEndTime(StatusEnum.FINALIZE, 1);
+
+		final LocalDateTime cutoffLocalDateTime = LocalDateTime.now()
+			.minusMinutes(0);
+		final Date cutoffDate = Date.from(cutoffLocalDateTime
+			.atZone(ZoneId.systemDefault())
+			.toInstant());
+
+		final List<JobInstance> jobInstancesByCutoff =
+			mySvc.fetchInstances(JOB_DEFINITION_ID, StatusEnum.getEndedStatuses(), cutoffDate, PageRequest.of(0, 100));
+
+		assertEquals(Set.of(completedId, failedId, erroredId, cancelledId),
+			jobInstancesByCutoff.stream()
+				.map(JobInstance::getInstanceId)
+				.collect(Collectors.toUnmodifiableSet()));
+	}
+
+	@Test
+	public void testFetchInstanceWithStatusAndCutoff_cutoffs() {
+		myCaptureQueriesListener.clear();
+
+		storeJobInstanceAndUpdateWithEndTime(StatusEnum.COMPLETED, 3);
+		storeJobInstanceAndUpdateWithEndTime(StatusEnum.COMPLETED, 4);
+		final String sevenMinutesAgoId = storeJobInstanceAndUpdateWithEndTime(StatusEnum.COMPLETED, 7);
+		final String eightMinutesAgoId = storeJobInstanceAndUpdateWithEndTime(StatusEnum.COMPLETED, 8);
+
+		final LocalDateTime cutoffLocalDateTime = LocalDateTime.now()
+			.minusMinutes(6);
+
+		final Date cutoffDate = Date.from(cutoffLocalDateTime
+			.atZone(ZoneId.systemDefault())
+			.toInstant());
+
+		final List<JobInstance> jobInstancesByCutoff =
+			mySvc.fetchInstances(JOB_DEFINITION_ID, StatusEnum.getEndedStatuses(), cutoffDate, PageRequest.of(0, 100));
+
+		myCaptureQueriesListener.logSelectQueries();
+		myCaptureQueriesListener.getSelectQueries().forEach(query -> ourLog.info("query: {}", query.getSql(true, true)));
+
+		assertEquals(Set.of(sevenMinutesAgoId, eightMinutesAgoId),
+			jobInstancesByCutoff.stream()
+				.map(JobInstance::getInstanceId)
+				.collect(Collectors.toUnmodifiableSet()));
+	}
+
+	@Test
+	public void testFetchInstanceWithStatusAndCutoff_pages() {
+		final String job1 = storeJobInstanceAndUpdateWithEndTime(StatusEnum.COMPLETED, 5);
+		final String job2 = storeJobInstanceAndUpdateWithEndTime(StatusEnum.COMPLETED, 5);
+		storeJobInstanceAndUpdateWithEndTime(StatusEnum.COMPLETED, 5);
+		storeJobInstanceAndUpdateWithEndTime(StatusEnum.COMPLETED, 5);
+		storeJobInstanceAndUpdateWithEndTime(StatusEnum.COMPLETED, 5);
+		storeJobInstanceAndUpdateWithEndTime(StatusEnum.COMPLETED, 5);
+
+		final LocalDateTime cutoffLocalDateTime = LocalDateTime.now()
+			.minusMinutes(0);
+
+		final Date cutoffDate = Date.from(cutoffLocalDateTime
+			.atZone(ZoneId.systemDefault())
+			.toInstant());
+
+		final List<JobInstance> jobInstancesByCutoff =
+			mySvc.fetchInstances(JOB_DEFINITION_ID, StatusEnum.getEndedStatuses(), cutoffDate, PageRequest.of(0, 2));
+
+		assertEquals(Set.of(job1, job2),
+			jobInstancesByCutoff.stream()
+				.map(JobInstance::getInstanceId)
+				.collect(Collectors.toUnmodifiableSet()));
+	}
+
 	/**
 	 * Returns a set of statuses, and whether they should be successfully picked up and started by a consumer.
 	 * @return
@@ -548,4 +631,29 @@ public class JpaJobPersistenceImplTest extends BaseJpaR4Test {
 		return instance;
 	}
 
+
+	@Nonnull
+	private String storeJobInstanceAndUpdateWithEndTime(StatusEnum theStatus, int minutes) {
+		final JobInstance jobInstance = new JobInstance();
+
+		jobInstance.setJobDefinitionId(JOB_DEFINITION_ID);
+		jobInstance.setStatus(theStatus);
+		jobInstance.setJobDefinitionVersion(JOB_DEF_VER);
+		jobInstance.setParameters(CHUNK_DATA);
+		jobInstance.setReport("TEST");
+
+		final String id = mySvc.storeNewInstance(jobInstance);
+
+		jobInstance.setInstanceId(id);
+		final LocalDateTime localDateTime = LocalDateTime.now()
+			.minusMinutes(minutes);
+		ourLog.info("localDateTime: {}", localDateTime);
+		jobInstance.setEndTime(Date.from(localDateTime
+			.atZone(ZoneId.systemDefault())
+			.toInstant()));
+
+		mySvc.updateInstance(jobInstance);
+
+		return id;
+	}
 }

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportTest.java

@@ -49,6 +49,7 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.concurrent.TimeUnit;
 import java.util.stream.Stream;
 
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
@@ -667,9 +668,11 @@ public class BulkDataExportTest extends BaseResourceProviderR4Test {
 		assertNotNull(startResponse);
 
 		// Run a scheduled pass to build the export
-		myBatch2JobHelper.awaitJobCompletion(startResponse.getJobId());
+		myBatch2JobHelper.awaitJobCompletion(startResponse.getJobId(), 60);
 
-		await().until(() -> myJobRunner.getJobInfo(startResponse.getJobId()).getReport() != null);
+		await()
+			.atMost(120, TimeUnit.SECONDS)
+			.until(() -> myJobRunner.getJobInfo(startResponse.getJobId()).getReport() != null);
 
 		// Iterate over the files
 		String report = myJobRunner.getJobInfo(startResponse.getJobId()).getReport();

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/bulk/BulkExportUseCaseTest.java

@@ -6,11 +6,15 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.api.model.BulkExportJobResults;
 import ca.uhn.fhir.jpa.api.svc.IBatch2JobRunner;
 import ca.uhn.fhir.jpa.batch.models.Batch2JobStartResponse;
+import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
 import ca.uhn.fhir.jpa.bulk.export.model.BulkExportResponseJson;
 import ca.uhn.fhir.jpa.provider.BaseResourceProviderR4Test;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.util.BulkExportUtils;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
 import ca.uhn.fhir.rest.api.server.bulk.BulkDataExportOptions;
 import ca.uhn.fhir.util.JsonUtil;
 import ca.uhn.fhir.util.SearchParameterUtil;
@@ -43,7 +47,7 @@ import org.springframework.beans.factory.annotation.Autowired;
 
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
-import java.util.Arrays;
+import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -51,9 +55,10 @@ import java.util.List;
 import java.util.Map;
 import java.util.Optional;
 import java.util.Set;
-import java.util.stream.Collectors;
 import java.util.concurrent.TimeUnit;
+import java.util.stream.Collectors;
 
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 import static org.awaitility.Awaitility.await;
 import static org.hamcrest.CoreMatchers.is;
 import static org.hamcrest.CoreMatchers.notNullValue;
@@ -61,12 +66,12 @@ import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.empty;
 import static org.hamcrest.Matchers.equalTo;
-import static org.hamcrest.Matchers.hasItem;
 import static org.hamcrest.Matchers.hasSize;
 import static org.hamcrest.Matchers.not;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.junit.jupiter.api.Assertions.fail;
 
 
 public class BulkExportUseCaseTest extends BaseResourceProviderR4Test {
@@ -164,7 +169,9 @@ public class BulkExportUseCaseTest extends BaseResourceProviderR4Test {
 			HttpGet statusGet = new HttpGet(pollingLocation);
 			String expectedOriginalUrl = myClient.getServerBase() + "/$export";
 			try (CloseableHttpResponse status = ourHttpClient.execute(statusGet)) {
+				assertEquals(200, status.getStatusLine().getStatusCode());
 				String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
+				assertTrue(isNotBlank(responseContent), responseContent);
 
 				ourLog.info(responseContent);
 
@@ -403,6 +410,7 @@ public class BulkExportUseCaseTest extends BaseResourceProviderR4Test {
 		@AfterEach
 		public void after() {
 			myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.DISABLED);
+			myDaoConfig.setBulkExportFileMaximumCapacity(DaoConfig.DEFAULT_BULK_EXPORT_FILE_MAXIMUM_CAPACITY);
 		}
 
 		@Test
@@ -430,6 +438,57 @@ public class BulkExportUseCaseTest extends BaseResourceProviderR4Test {
 			assertThat(typeToContents.get("Observation"), containsString("obs-included"));
 			assertThat(typeToContents.get("Observation"), not(containsString("obs-excluded")));
 		}
+
+		@Test
+		public void testBulkExportWithLowMaxFileCapacity() {
+			final int numPatients = 250;
+			myDaoConfig.setBulkExportFileMaximumCapacity(1);
+			myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.ENABLED);
+
+			RequestDetails details = new SystemRequestDetails();
+			List<String> patientIds = new ArrayList<>();
+			for(int i = 0; i < numPatients; i++){
+				String id = "p-"+i;
+				Patient patient = new Patient();
+				patient.setId(id);
+				myPatientDao.update(patient, details);
+				patientIds.add(id);
+			}
+
+			int patientsCreated = myPatientDao.search(SearchParameterMap.newSynchronous(), details).size();
+			assertEquals(numPatients, patientsCreated);
+
+			BulkDataExportOptions options = new BulkDataExportOptions();
+			options.setResourceTypes(Sets.newHashSet("Patient"));
+			options.setExportStyle(BulkDataExportOptions.ExportStyle.PATIENT);
+			options.setOutputFormat(Constants.CT_FHIR_NDJSON);
+
+			Batch2JobStartResponse job = myJobRunner.startNewJob(BulkExportUtils.createBulkExportJobParametersFromExportOptions(options));
+			myBatch2JobHelper.awaitJobCompletion(job.getJobId(), 60);
+			ourLog.debug("Job status after awaiting - {}", myJobRunner.getJobInfo(job.getJobId()).getStatus());
+			await()
+				.atMost(300, TimeUnit.SECONDS)
+				.until(() -> {
+					BulkExportJobStatusEnum status = myJobRunner.getJobInfo(job.getJobId()).getStatus();
+					if (!BulkExportJobStatusEnum.COMPLETE.equals(status)) {
+						fail("Job status was changed from COMPLETE to " + status);
+					}
+					return myJobRunner.getJobInfo(job.getJobId()).getReport() != null;
+				});
+
+			String report = myJobRunner.getJobInfo(job.getJobId()).getReport();
+			BulkExportJobResults results = JsonUtil.deserialize(report, BulkExportJobResults.class);
+			List<String> binaryUrls = results.getResourceTypeToBinaryIds().get("Patient");
+
+			IParser jsonParser = myFhirContext.newJsonParser();
+			for(String url : binaryUrls){
+				Binary binary = myClient.read().resource(Binary.class).withUrl(url).execute();
+				assertEquals(Constants.CT_FHIR_NDJSON, binary.getContentType());
+				String resourceContents = new String(binary.getContent(), Constants.CHARSET_UTF8);
+				String resourceId = jsonParser.parseResource(resourceContents).getIdElement().getIdPart();
+				assertTrue(patientIds.contains(resourceId));
+			}
+		}
 	}
 
 

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java

@@ -9,6 +9,7 @@ import ca.uhn.fhir.batch2.model.StatusEnum;
 import ca.uhn.fhir.interceptor.api.IAnonymousInterceptor;
 import ca.uhn.fhir.interceptor.api.Pointcut;
 import ca.uhn.fhir.jpa.batch.models.Batch2JobStartResponse;
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
 import ca.uhn.fhir.jpa.test.PatientReindexTestHelper;
@@ -23,15 +24,19 @@ import org.junit.jupiter.params.provider.MethodSource;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import javax.annotation.PostConstruct;
+import java.util.Date;
 import java.util.List;
 import java.util.stream.Stream;
 
 import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.equalTo;
 import static org.hamcrest.Matchers.hasSize;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
 public class ReindexJobTest extends BaseJpaR4Test {
 
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ReindexJobTest.class);
+
 	@Autowired
 	private IJobCoordinator myJobCoordinator;
 
@@ -89,6 +94,41 @@ public class ReindexJobTest extends BaseJpaR4Test {
 		myDaoConfig.setMarkResourcesForReindexingUponSearchParameterChange(reindexPropertyCache);
 	}
 
+	@Test
+	public void testReindexDeletedResources_byUrl_willRemoveDeletedResourceEntriesFromIndexTables(){
+		IIdType obsId = myReindexTestHelper.createObservationWithAlleleExtension(Observation.ObservationStatus.FINAL);
+
+		runInTransaction(() -> {
+			int entriesInSpIndexTokenTable = myResourceIndexedSearchParamTokenDao.countForResourceId(obsId.getIdPartAsLong());
+			assertThat(entriesInSpIndexTokenTable, equalTo(1));
+
+			// simulate resource deletion
+			ResourceTable resource = myResourceTableDao.findById(obsId.getIdPartAsLong()).get();
+			Date currentDate = new Date();
+			resource.setDeleted(currentDate);
+			resource.setUpdated(currentDate);
+			resource.setHashSha256(null);
+			resource.setVersion(2L);
+			myResourceTableDao.save(resource);
+		});
+
+		// execute reindexing
+		ReindexJobParameters parameters = new ReindexJobParameters();
+		parameters.addUrl("Observation?status=final");
+
+		JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
+		startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
+		startRequest.setParameters(parameters);
+		Batch2JobStartResponse res = myJobCoordinator.startInstance(startRequest);
+		myBatch2JobHelper.awaitJobCompletion(res);
+
+		// then
+		runInTransaction(() -> {
+			int entriesInSpIndexTokenTablePostReindexing = myResourceIndexedSearchParamTokenDao.countForResourceId(obsId.getIdPartAsLong());
+			assertThat(entriesInSpIndexTokenTablePostReindexing, equalTo(0));
+		});
+	}
+
 	@Test
 	public void testReindex_Everything() {
 		// setup

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/DiffProviderR4Test.java

@@ -47,8 +47,8 @@ public class DiffProviderR4Test extends BaseResourceProviderR4Test {
 
 		Assertions.assertEquals("replace", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 0, "operation", "type"));
 		Assertions.assertEquals("Patient.text.div", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 0, "operation", "path"));
-		Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"><table class=\"hapiPropertyTable\"><tbody/></table></div>", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 0, "operation", "previousValue"));
+		Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"><table class=\"hapiPropertyTable\"><tbody></tbody></table></div>", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 0, "operation", "previousValue"));
-		Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\"><b>SMITH </b></div><table class=\"hapiPropertyTable\"><tbody/></table></div>", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 0, "operation", "value"));
+		Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\"><b>SMITH </b></div><table class=\"hapiPropertyTable\"><tbody></tbody></table></div>", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 0, "operation", "value"));
 
 		Assertions.assertEquals("insert", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 1, "operation", "type"));
 		Assertions.assertEquals("Patient.name", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 1, "operation", "path"));
@@ -86,8 +86,8 @@ public class DiffProviderR4Test extends BaseResourceProviderR4Test {
 
 		Assertions.assertEquals("replace", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 2, "operation", "type"));
 		Assertions.assertEquals("Patient.text.div", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 2, "operation", "path"));
-		Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"><table class=\"hapiPropertyTable\"><tbody/></table></div>", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 2, "operation", "previousValue"));
+		Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"><table class=\"hapiPropertyTable\"><tbody></tbody></table></div>", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 2, "operation", "previousValue"));
-		Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\"><b>SMITH </b></div><table class=\"hapiPropertyTable\"><tbody/></table></div>", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 2, "operation", "value"));
+		Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\"><b>SMITH </b></div><table class=\"hapiPropertyTable\"><tbody></tbody></table></div>", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 2, "operation", "value"));
 
 		Assertions.assertEquals("insert", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 3, "operation", "type"));
 		Assertions.assertEquals("Patient.name", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 3, "operation", "path"));

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ExpungeR4Test.java

@@ -9,6 +9,9 @@ import ca.uhn.fhir.jpa.dao.data.ISearchDao;
 import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
 import ca.uhn.fhir.jpa.dao.expunge.ExpungeService;
 import ca.uhn.fhir.jpa.delete.ThreadSafeResourceDeleterSvc;
+import ca.uhn.fhir.jpa.entity.TermCodeSystem;
+import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
+import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
 import ca.uhn.fhir.jpa.model.entity.NormalizedQuantitySearchLevel;
 import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
@@ -35,6 +38,7 @@ import org.apache.http.client.methods.HttpDelete;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.BooleanType;
+import org.hl7.fhir.r4.model.CodeSystem;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.DateType;
 import org.hl7.fhir.r4.model.DecimalType;
@@ -46,6 +50,7 @@ import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Quantity;
 import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.SearchParameter;
+import org.hl7.fhir.r4.model.StringType;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
@@ -58,11 +63,13 @@ import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
 import java.util.List;
 
+import static ca.uhn.fhir.batch2.jobs.termcodesystem.TermCodeSystemJobConfig.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
 import static org.awaitility.Awaitility.await;
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.empty;
 import static org.hamcrest.Matchers.not;
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotEquals;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
@@ -77,6 +84,9 @@ public class ExpungeR4Test extends BaseResourceProviderR4Test {
 	private IIdType myOneVersionObservationId;
 	private IIdType myTwoVersionObservationId;
 	private IIdType myDeletedObservationId;
+	private IIdType myOneVersionCodeSystemId;
+	private IIdType myTwoVersionCodeSystemIdV1;
+	private IIdType myTwoVersionCodeSystemIdV2;
 	@Autowired
 	private ISearchDao mySearchEntityDao;
 	@Autowired
@@ -200,6 +210,40 @@ public class ExpungeR4Test extends BaseResourceProviderR4Test {
 
 	}
 
+	public void createStandardCodeSystems() {
+		CodeSystem codeSystem1 = new CodeSystem();
+		codeSystem1.setUrl(URL_MY_CODE_SYSTEM);
+		codeSystem1.setName("CS1-V1");
+		codeSystem1.setVersion("1");
+		codeSystem1.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
+		codeSystem1
+			.addConcept().setCode("C").setDisplay("Code C").addDesignation(
+				new CodeSystem.ConceptDefinitionDesignationComponent().setLanguage("en").setValue("CodeCDesignation")).addProperty(
+				new CodeSystem.ConceptPropertyComponent().setCode("CodeCProperty").setValue(new StringType("CodeCPropertyValue"))
+			)
+			.addConcept(new CodeSystem.ConceptDefinitionComponent().setCode("CA").setDisplay("Code CA")
+				.addConcept(new CodeSystem.ConceptDefinitionComponent().setCode("CAA").setDisplay("Code CAA"))
+			)
+			.addConcept(new CodeSystem.ConceptDefinitionComponent().setCode("CB").setDisplay("Code CB"));
+		codeSystem1
+			.addConcept().setCode("D").setDisplay("Code D");
+		myOneVersionCodeSystemId = myCodeSystemDao.create(codeSystem1).getId();
+
+		CodeSystem cs2v1 = new CodeSystem();
+		cs2v1.setUrl(URL_MY_CODE_SYSTEM_2);
+		cs2v1.setVersion("1");
+		cs2v1.setName("CS2-V1");
+		cs2v1.addConcept().setCode("E").setDisplay("Code E");
+		myTwoVersionCodeSystemIdV1 = myCodeSystemDao.create(cs2v1).getId();
+
+		CodeSystem cs2v2 = new CodeSystem();
+		cs2v2.setUrl(URL_MY_CODE_SYSTEM_2);
+		cs2v2.setVersion("2");
+		cs2v2.setName("CS2-V2");
+		cs2v2.addConcept().setCode("F").setDisplay("Code F");
+		myTwoVersionCodeSystemIdV2 = myCodeSystemDao.create(cs2v2).getId();
+	}
+
 	private IFhirResourceDao<?> getDao(IIdType theId) {
 		IFhirResourceDao<?> dao;
 		switch (theId.getResourceType()) {
@@ -209,6 +253,9 @@ public class ExpungeR4Test extends BaseResourceProviderR4Test {
 			case "Observation":
 				dao = myObservationDao;
 				break;
+			case "CodeSystem":
+				dao = myCodeSystemDao;
+				break;
 			default:
 				fail("Restype: " + theId.getResourceType());
 				dao = myPatientDao;
@@ -809,6 +856,38 @@ public class ExpungeR4Test extends BaseResourceProviderR4Test {
 		assertTrue(actualRemainingPatientHistoryRecords <= maximumRemainingPatientHistoryRecords);
 	}
 
+	@Test
+	public void testDeleteCodeSystemByUrlThenExpunge() {
+		createStandardCodeSystems();
+
+		myCodeSystemDao.deleteByUrl("CodeSystem?url=" + URL_MY_CODE_SYSTEM, null);
+		myTerminologyDeferredStorageSvc.saveDeferred();
+		myBatch2JobHelper.awaitAllJobsOfJobDefinitionIdToComplete(TERM_CODE_SYSTEM_DELETE_JOB_NAME);
+		myCodeSystemDao.expunge(new ExpungeOptions()
+			.setExpungeDeletedResources(true)
+			.setExpungeOldVersions(true), null);
+
+		assertExpunged(myOneVersionCodeSystemId);
+		assertStillThere(myTwoVersionCodeSystemIdV1);
+		assertStillThere(myTwoVersionCodeSystemIdV2);
+		runInTransaction(() -> {
+			verifyOneVersionCodeSystemChildrenExpunged();
+			verifyTwoVersionCodeSystemV1AndChildrenStillThere();
+			verifyTwoVersionCodeSystemV2AndChildrenStillThere();
+		});
+
+		myCodeSystemDao.deleteByUrl("CodeSystem?url=" + URL_MY_CODE_SYSTEM_2, null);
+		myTerminologyDeferredStorageSvc.saveDeferred();
+		myBatch2JobHelper.awaitAllJobsOfJobDefinitionIdToComplete(TERM_CODE_SYSTEM_DELETE_JOB_NAME);
+		myCodeSystemDao.expunge(new ExpungeOptions()
+			.setExpungeDeletedResources(true)
+			.setExpungeOldVersions(true), null);
+
+		assertExpunged(myTwoVersionCodeSystemIdV1);
+		assertExpunged(myTwoVersionCodeSystemIdV2);
+		runInTransaction(this::verifyCodeSystemsAndChildrenExpunged);
+	}
+
 	private List<Patient> createPatientsWithForcedIds(int theNumPatients) {
 		RequestDetails requestDetails = new SystemRequestDetails();
 		List<Patient> createdPatients = new ArrayList<>();
@@ -839,4 +918,60 @@ public class ExpungeR4Test extends BaseResourceProviderR4Test {
 			myPatientDao.delete(patient.getIdElement(), requestDetails);
 		}
 	}
+
+	private void verifyOneVersionCodeSystemChildrenExpunged() {
+		List<TermCodeSystemVersion> myOneVersionCodeSystemVersions = myTermCodeSystemVersionDao.findByCodeSystemResourcePid(myOneVersionCodeSystemId.getIdPartAsLong());
+		assertEquals(0, myOneVersionCodeSystemVersions.size());
+		assertThat(myTermConceptDesignationDao.findAll(), empty());
+		assertThat(myTermConceptPropertyDao.findAll(), empty());
+		assertThat(myTermConceptParentChildLinkDao.findAll(), empty());
+		List<TermConcept> existingCodeSystemConcepts = myTermConceptDao.findAll();
+		for (TermConcept tc : existingCodeSystemConcepts) {
+			if (tc.getCode().charAt(0) == 'C' || tc.getCode().charAt(0) == 'D') {
+				fail();
+			}
+		}
+	}
+
+	private void verifyTwoVersionCodeSystemV1AndChildrenStillThere() {
+		TermCodeSystem myTwoVersionCodeSystem = myTermCodeSystemDao.findByResourcePid(myTwoVersionCodeSystemIdV2.getIdPartAsLong());
+		TermCodeSystemVersion myTwoVersionCodeSystemVersion1 = verifyTermCodeSystemVersionExistsWithDisplayName("CS2-V1");
+		assertNotEquals(myTwoVersionCodeSystem.getCurrentVersion().getPid(), myTwoVersionCodeSystemVersion1.getPid());
+		List<TermConcept> myTwoVersionCodeSystemVersion1Concepts = new ArrayList(myTwoVersionCodeSystemVersion1.getConcepts());
+		assertEquals(1, myTwoVersionCodeSystemVersion1Concepts.size());
+		TermConcept conceptE = myTwoVersionCodeSystemVersion1Concepts.get(0);
+		assertEquals("E", conceptE.getCode());
+	}
+
+	private void verifyTwoVersionCodeSystemV2AndChildrenStillThere() {
+		TermCodeSystem myTwoVersionCodeSystem = myTermCodeSystemDao.findByResourcePid(myTwoVersionCodeSystemIdV2.getIdPartAsLong());
+		TermCodeSystemVersion myTwoVersionCodeSystemVersion2 = verifyTermCodeSystemVersionExistsWithDisplayName("CS2-V2");
+		assertEquals(myTwoVersionCodeSystem.getCurrentVersion().getPid(), myTwoVersionCodeSystemVersion2.getPid());
+		List<TermConcept> myTwoVersionCodeSystemVersion2Concepts = new ArrayList(myTwoVersionCodeSystemVersion2.getConcepts());
+		assertEquals(1, myTwoVersionCodeSystemVersion2Concepts.size());
+		TermConcept conceptF = myTwoVersionCodeSystemVersion2Concepts.get(0);
+		assertEquals("F", conceptF.getCode());
+	}
+
+	private TermCodeSystemVersion verifyTermCodeSystemVersionExistsWithDisplayName(String theDisplayName) {
+		List<TermCodeSystemVersion> myCodeSystemVersions = myTermCodeSystemVersionDao.findAll();
+		for (TermCodeSystemVersion csv : myCodeSystemVersions) {
+			if (csv.getCodeSystemDisplayName().equals(theDisplayName)) {
+				return csv;
+			}
+		}
+		fail();
+		return null;
+	}
+
+	private void verifyCodeSystemsAndChildrenExpunged() {
+		assertThat(myTermCodeSystemVersionDao.findAll(), empty());
+		assertThat(myTermConceptDesignationDao.findAll(), empty());
+		assertThat(myTermConceptPropertyDao.findAll(), empty());
+		assertThat(myTermConceptParentChildLinkDao.findAll(), empty());
+		assertThat(myTermConceptDao.findAll(), empty());
+		assertThat(myResourceTableDao.findAll(), empty());
+		assertThat(myResourceHistoryTableDao.findAll(), empty());
+		assertThat(myForcedIdDao.findAll(), empty());
+	}
 }

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java

@@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.provider.r4;
 import ca.uhn.fhir.i18n.HapiLocalizer;
 import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
 import ca.uhn.fhir.jpa.dao.data.ISearchDao;
 import ca.uhn.fhir.jpa.entity.Search;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
@@ -12,6 +13,7 @@ import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.jpa.model.util.UcumServiceUtil;
 import ca.uhn.fhir.jpa.provider.BaseResourceProviderR4Test;
 import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.term.ZipCollectionBuilder;
 import ca.uhn.fhir.jpa.test.config.TestR4Config;
 import ca.uhn.fhir.jpa.util.QueryParameterUtils;
@@ -27,6 +29,7 @@ import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.api.PreferReturnEnum;
 import ca.uhn.fhir.rest.api.SearchTotalModeEnum;
 import ca.uhn.fhir.rest.api.SummaryEnum;
+import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
 import ca.uhn.fhir.rest.client.apache.ResourceEntity;
 import ca.uhn.fhir.rest.client.api.IClientInterceptor;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
@@ -309,12 +312,10 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 		assertNotNull(id);
 		assertEquals("resource-security", id.getIdPart());
-
 	}
 
 	@Test
 	public void createSearchParameter_with2Expressions_succeeds() {
-
 		SearchParameter searchParameter = new SearchParameter();
 
 		searchParameter.setStatus(Enumerations.PublicationStatus.ACTIVE);
@@ -326,7 +327,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		MethodOutcome result = myClient.create().resource(searchParameter).execute();
 
 		assertEquals(true, result.getCreated());
-
 	}
 
 	@Test
@@ -454,7 +454,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			assertThat(output, containsString(MSG_PREFIX_INVALID_FORMAT + "">""));
 			assertEquals(400, resp.getStatusLine().getStatusCode());
 		}
-
 	}
 
 
@@ -764,6 +763,8 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 	public void testUpdateResourceAfterReadOperationAndNoChangesShouldNotChangeVersion(){
 		// Create Patient
 		Patient patient = new Patient();
+		patient.getText().setDivAsString("<div xmlns=\"http://www.w3.org/1999/xhtml\">hello</div>");
+
 		patient = (Patient) myClient.create().resource(patient).execute().getResource();
 		assertEquals(1, patient.getIdElement().getVersionIdPartAsLong());
 
@@ -909,7 +910,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 	@Test
 	@Disabled
-	public void test() throws IOException {
+	public void testMakingQuery() throws IOException {
 		HttpGet get = new HttpGet(myServerBase + "/QuestionnaireResponse?_count=50&status=completed&questionnaire=ARIncenterAbsRecord&_lastUpdated=%3E" + UrlUtil.escapeUrlParam("=2018-01-01") + "&context.organization=O3435");
 		ourLog.info("*** MAKING QUERY");
 		ourHttpClient.execute(get);
@@ -7554,6 +7555,113 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 		assertTrue(resultIds.contains("Patient/" + patientId + "/_history/2"));
 	}
 
+
+	private static class CreateResourceInput {
+		boolean IsEnforceRefOnWrite;
+		boolean IsEnforceRefOnType;
+		boolean IsAutoCreatePlaceholderReferences;
+
+		public CreateResourceInput(
+			boolean theEnforceRefOnWrite,
+			boolean theEnforceRefOnType,
+			boolean theAutoCreatePlaceholders
+		) {
+			IsEnforceRefOnWrite = theEnforceRefOnWrite;
+			IsEnforceRefOnType = theEnforceRefOnType;
+			IsAutoCreatePlaceholderReferences = theAutoCreatePlaceholders;
+		}
+
+		@Override
+		public String toString() {
+			return "IsEnforceReferentialIntegrityOnWrite : "
+				+ IsEnforceRefOnWrite + "\n"
+				+ "IsEnforceReferenceTargetTypes : "
+				+ IsEnforceRefOnType + "\n"
+				+ "IsAutoCreatePlaceholderReferenceTargets : "
+				+ IsAutoCreatePlaceholderReferences + "\n";
+		}
+	}
+
+	private static List<CreateResourceInput> createResourceParameters() {
+		boolean[] bools = new boolean[] { true, false };
+		List<CreateResourceInput> input = new ArrayList<>();
+		for (boolean bool : bools) {
+			for (boolean bool2 : bools) {
+				for (boolean bool3 : bools) {
+					input.add(new CreateResourceInput(bool, bool2, bool3));
+				}
+			}
+		}
+		return input;
+	}
+
+	@ParameterizedTest
+	@MethodSource("createResourceParameters")
+	public void createResource_refIntegrityOnWriteAndRefTargetTypes_throws(CreateResourceInput theInput) {
+		ourLog.info(
+			String.format("Test case : \n%s", theInput.toString())
+		);
+
+		String patientStr = """
+			{
+			  "resourceType": "Patient",
+			  "managingOrganization": {
+			    "reference": "urn:uuid:d8080e87-1842-46b4-aea0-b65803bc2897"
+			  }
+			}
+			""";
+		IParser parser = myFhirContext.newJsonParser();
+		Patient patient = parser.parseResource(Patient.class, patientStr);
+
+		{
+			List<IBaseResource> orgs = myOrganizationDao
+				.search(new SearchParameterMap(), new SystemRequestDetails())
+				.getAllResources();
+
+			assertTrue(orgs == null || orgs.isEmpty());
+		}
+
+		boolean isEnforceRefOnWrite = myDaoConfig.isEnforceReferentialIntegrityOnWrite();
+		boolean isEnforceRefTargetTypes = myDaoConfig.isEnforceReferenceTargetTypes();
+		boolean isAutoCreatePlaceholderReferences = myDaoConfig.isAutoCreatePlaceholderReferenceTargets();
+
+		try {
+			// allows resources to be created even if they have local resources that do not exist
+			myDaoConfig.setEnforceReferentialIntegrityOnWrite(theInput.IsEnforceRefOnWrite);
+			// ensures target references are using the correct resource type
+			myDaoConfig.setEnforceReferenceTargetTypes(theInput.IsEnforceRefOnType);
+			// will create the resource if it does not already exist
+			myDaoConfig.setAutoCreatePlaceholderReferenceTargets(theInput.IsAutoCreatePlaceholderReferences);
+
+			// should fail
+			DaoMethodOutcome result = myPatientDao.create(patient, new SystemRequestDetails());
+
+			// a bad reference can never create a new resource
+			{
+				List<IBaseResource> orgs = myOrganizationDao
+					.search(new SearchParameterMap(), new SystemRequestDetails())
+					.getAllResources();
+
+				assertTrue(orgs == null || orgs.isEmpty());
+			}
+
+			// only if all 3 are true do we expect this to fail
+			assertFalse(
+				theInput.IsAutoCreatePlaceholderReferences
+				&& theInput.IsEnforceRefOnType
+				&& theInput.IsEnforceRefOnWrite
+			);
+		} catch (InvalidRequestException ex) {
+			assertTrue(ex.getMessage().contains(
+				"Invalid resource reference"
+			), ex.getMessage());
+		} finally {
+			myDaoConfig.setEnforceReferentialIntegrityOnWrite(isEnforceRefOnWrite);
+			myDaoConfig.setEnforceReferenceTargetTypes(isEnforceRefTargetTypes);
+			myDaoConfig.setAutoCreatePlaceholderReferenceTargets(isAutoCreatePlaceholderReferences);
+		}
+	}
+
 	@Test
 	public void searchResource_bySourceWithPreserveRequestIdDisabled_isSuccess() {
 		String sourceUri = "http://acme.org";
@@ -8083,5 +8191,4 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 			);
 		}
 	}
-
 }

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java

@@ -477,6 +477,7 @@ public class TerminologySvcImplR4Test extends BaseTermR4Test {
 		myCodeSystemDao.update(codeSystem, mySrd);
 
 		await().until(() -> {
+			myBatch2JobHelper.runMaintenancePass();
 			myTerminologyDeferredStorageSvc.saveAllDeferred();
 			return myTerminologyDeferredStorageSvc.isStorageQueueEmpty(true);
 			}, equalTo(true));

hapi-fhir-jpaserver-test-r4b/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-test-r5/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/provider/r5/ResourceProviderR5Test.java

@@ -227,19 +227,12 @@ public class ResourceProviderR5Test extends BaseResourceProviderR5Test {
 		try (CloseableHttpResponse resp = ourHttpClient.execute(post)) {
 			String respString = IOUtils.toString(resp.getEntity().getContent(), Charsets.UTF_8);
 			ourLog.debug(respString);
-//			assertEquals(200, resp.getStatusLine().getStatusCode());
+			assertEquals(200, resp.getStatusLine().getStatusCode());
 
+			// As of 2023-01-26, the above line was restored.
 			// As of 2021-12-28, the R5 structures return a version string that isn't
 			// actually in the fhirVersion ValueSet. If this stops being the case this
 			// test will fail and the line above should be restored
-			OperationOutcome oo = myFhirCtx.newJsonParser().parseResource(OperationOutcome.class, respString);
-			assertEquals(1, oo.getIssue().size());
-//			assertThat(oo.getIssue().get(0).getDiagnostics(), containsString("is not in the value set 'FHIRVersion'"));
-			//As of 2022-10-06, the error is now that RequestGroup is not in the resourcetypes valueset, (though it is).
-
-			//TODO JA: I'm not sure if i have to update this valueset somewhere? the linked valueset _does_ contain the resource type.
-			assertThat(oo.getIssue().get(0).getDiagnostics(), containsString("is not in the value set 'Resource Types'"));
-
 
 		}
 	}

hapi-fhir-jpaserver-test-utilities/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>6.5.0-SNAPSHOT</version>
+		<version>6.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/BaseJpaR4Test.java

@@ -60,6 +60,7 @@ import ca.uhn.fhir.jpa.dao.data.ISearchIncludeDao;
 import ca.uhn.fhir.jpa.dao.data.ISearchParamPresentDao;
 import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
 import ca.uhn.fhir.jpa.dao.data.ITagDefinitionDao;
+import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
 import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
 import ca.uhn.fhir.jpa.dao.data.ITermConceptDesignationDao;
 import ca.uhn.fhir.jpa.dao.data.ITermConceptMapDao;
@@ -216,6 +217,7 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
 	public static final String MY_VALUE_SET = "my-value-set";
 	public static final String URL_MY_VALUE_SET = "http://example.com/my_value_set";
 	public static final String URL_MY_CODE_SYSTEM = "http://example.com/my_code_system";
+	public static final String URL_MY_CODE_SYSTEM_2 = "http://example.com/my_code_system_2";
 
 	@Autowired
 	protected IPackageInstallerSvc myPackageInstallerSvc;
@@ -293,6 +295,8 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
 	@Qualifier("myCodeSystemDaoR4")
 	protected IFhirResourceDaoCodeSystem<CodeSystem> myCodeSystemDao;
 	@Autowired
+	protected ITermCodeSystemDao myTermCodeSystemDao;
+	@Autowired
 	protected ITermConceptParentChildLinkDao myTermConceptParentChildLinkDao;
 	@Autowired
 	@Qualifier("myCompartmentDefinitionDaoR4")

hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/Batch2JobHelper.java

@@ -71,7 +71,6 @@ public class Batch2JobHelper {
 		return awaitJobHasStatusWithoutMaintenancePass(theBatchJobId, StatusEnum.COMPLETED);
 	}
 
-
 	public JobInstance awaitJobCancelled(String theBatchJobId) {
 		return awaitJobHasStatus(theBatchJobId, StatusEnum.CANCELLED);
 	}
@@ -106,7 +105,6 @@ public class Batch2JobHelper {
 		return myJobCoordinator.getInstance(theBatchJobId);
 	}
 
-
 	public JobInstance awaitJobawaitJobHasStatusWithoutMaintenancePass(String theBatchJobId, int theSecondsToWait, StatusEnum... theExpectedStatus) {
 		assert !TransactionSynchronizationManager.isActualTransactionActive();
 
@@ -168,7 +166,6 @@ public class Batch2JobHelper {
 	public long getCombinedRecordsProcessed(String theJobId) {
 		JobInstance job = myJobCoordinator.getInstance(theJobId);
 		return job.getCombinedRecordsProcessed();
-
 	}
 
 	public void awaitAllJobsOfJobDefinitionIdToComplete(String theJobDefinitionId) {
@@ -243,6 +240,14 @@ public class Batch2JobHelper {
 		myJobMaintenanceService.runMaintenancePass();
 	}
 
+	/**
+	 * Forces a run of the maintenance pass without waiting for
+	 * the semaphore to release
+	 */
+	public void forceRunMaintenancePass() {
+		myJobMaintenanceService.forceMaintenancePass();
+	}
+
 	public void cancelAllJobsAndAwaitCancellation() {
 		List<JobInstance> instances = myJobPersistence.fetchInstances(1000, 0);
 		for (JobInstance next : instances) {