Merge branch 'jpa_migration'

example-projects/hapi-fhir-base-example-embedded-ws/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</version>
 		<relativePath>../../pom.xml</relativePath>
 	</parent>
 

example-projects/hapi-fhir-jpaserver-cds-example/pom.xml

@@ -10,7 +10,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</version>
 		<relativePath>../../pom.xml</relativePath>
 	</parent>
 

example-projects/hapi-fhir-jpaserver-dynamic/pom.xml

@@ -10,7 +10,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</version>
 	   <relativePath>../../pom.xml</relativePath>
 	</parent>
 

example-projects/hapi-fhir-jpaserver-example-postgres/pom.xml

@@ -10,7 +10,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</version>
 		<relativePath>../../pom.xml</relativePath>
 	</parent>
 	

example-projects/hapi-fhir-standalone-overlay-example/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</version>
 		<relativePath>../../pom.xml</relativePath>
 	</parent>
 	<artifactId>hapi-fhir-standalone-overlay-example</artifactId>

examples/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-deployable-pom/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</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>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</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>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
@@ -63,6 +63,10 @@
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-lang3</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-text</artifactId>
+		</dependency>
 		<dependency>
 			<groupId>commons-codec</groupId>
 			<artifactId>commons-codec</artifactId>

hapi-fhir-base/src/main/java/ca/uhn/fhir/context/ModelScanner.java

@@ -178,7 +178,7 @@ class ModelScanner {
 	}
 
 	/**
-	 * There are two implementations of all of the annotations (e.g. {@link Child} and {@link org.hl7.fhir.instance.model.annotations.Child}) since the HL7.org ones will eventually replace the HAPI
+	 * There are two implementations of all of the annotations (e.g. {@link Child} since the HL7.org ones will eventually replace the HAPI
 	 * ones. Annotations can't extend each other or implement interfaces or anything like that, so rather than duplicate all of the annotation processing code this method just creates an interface
 	 * Proxy to simulate the HAPI annotations if the HL7.org ones are found instead.
 	 */
@@ -482,9 +482,8 @@ class ModelScanner {
 	static Set<Class<? extends IBase>> scanVersionPropertyFile(Set<Class<? extends IBase>> theDatatypes, Map<String, Class<? extends IBaseResource>> theResourceTypes, FhirVersionEnum theVersion, Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> theExistingElementDefinitions) {
 		Set<Class<? extends IBase>> retVal = new HashSet<Class<? extends IBase>>();
 
-		InputStream str = theVersion.getVersionImplementation().getFhirVersionPropertiesFile();
-		Properties prop = new Properties();
-		try {
+		try (InputStream str = theVersion.getVersionImplementation().getFhirVersionPropertiesFile()) {
+			Properties prop = new Properties();
 			prop.load(str);
 			for (Entry<Object, Object> nextEntry : prop.entrySet()) {
 				String nextKey = nextEntry.getKey().toString();
@@ -542,8 +541,6 @@ class ModelScanner {
 			}
 		} catch (IOException e) {
 			throw new ConfigurationException("Failed to load model property file from classpath: " + "/ca/uhn/fhir/model/dstu/model.properties");
-		} finally {
-			IOUtils.closeQuietly(str);
 		}
 
 		return retVal;

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/VersionEnum.java

@@ -0,0 +1,8 @@
+package ca.uhn.fhir.util;
+
+public enum VersionEnum {
+
+	V3_4_0,
+	V3_5_0
+
+}

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/VersionUtil.java

@@ -23,8 +23,6 @@ package ca.uhn.fhir.util;
 import java.io.InputStream;
 import java.util.Properties;
 
-import org.apache.commons.io.IOUtils;
-
 /**
  * Used internally by HAPI to log the version of the HAPI FHIR framework
  * once, when the framework is first loaded by the classloader.
@@ -43,17 +41,13 @@ public class VersionUtil {
 	}
 
 	private static void initialize() {
-		InputStream is = null;
-		try {
-			is = VersionUtil.class.getResourceAsStream("/ca/uhn/fhir/hapi-version.properties");
+		try (InputStream is = VersionUtil.class.getResourceAsStream("/ca/uhn/fhir/hapi-version.properties")) {
 			Properties p = new Properties();
 			p.load(is);
 			ourVersion = p.getProperty("version");
 			ourLog.info("HAPI FHIR version is: " + ourVersion);
 		} catch (Exception e) {
 			ourLog.warn("Unable to determine HAPI version information", e);
-		} finally {
-			IOUtils.closeQuietly(is);
 		}
 	}
 	

hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/SchemaBaseValidator.java

@@ -212,7 +212,6 @@ public class SchemaBaseValidator implements IValidatorModule {
 
 				InputStream baseIs = FhirValidator.class.getResourceAsStream(pathToBase);
 				if (baseIs == null) {
-					IOUtils.closeQuietly(baseIs);
 					throw new InternalErrorException("Schema file not found: " + pathToBase);
 				}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/schematron/SchematronBaseValidator.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.validation.schematron;
  * 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.
@@ -30,12 +30,14 @@ import com.helger.commons.error.list.IErrorList;
 import com.helger.schematron.ISchematronResource;
 import com.helger.schematron.SchematronHelper;
 import com.helger.schematron.xslt.SchematronResourceSCH;
-import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.oclc.purl.dsdl.svrl.SchematronOutputType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import javax.xml.transform.stream.StreamSource;
+import java.io.IOException;
 import java.io.InputStream;
 import java.io.StringReader;
 import java.util.HashMap;
@@ -49,9 +51,13 @@ import java.util.Map;
  */
 public class SchematronBaseValidator implements IValidatorModule {
 
-	private Map<Class<? extends IBaseResource>, ISchematronResource> myClassToSchematron = new HashMap<Class<? extends IBaseResource>, ISchematronResource>();
+	private static final Logger ourLog = LoggerFactory.getLogger(SchematronBaseValidator.class);
+	private final Map<Class<? extends IBaseResource>, ISchematronResource> myClassToSchematron = new HashMap<>();
 	private FhirContext myCtx;
 
+	/**
+	 * Constructor
+	 */
 	public SchematronBaseValidator(FhirContext theContext) {
 		myCtx = theContext;
 	}
@@ -66,7 +72,7 @@ public class SchematronBaseValidator implements IValidatorModule {
 				validateResource(ValidationContext.subContext(theCtx, nextSubResource));
 			}
 		}
-		
+
 		ISchematronResource sch = getSchematron(theCtx);
 		String resourceAsString;
 		if (theCtx.getResourceAsStringEncoding() == EncodingEnum.XML) {
@@ -127,15 +133,14 @@ public class SchematronBaseValidator implements IValidatorModule {
 			}
 
 			String pathToBase = myCtx.getVersion().getPathToSchemaDefinitions() + '/' + theCtx.getFhirContext().getResourceDefinition(theCtx.getResource()).getBaseDefinition().getName().toLowerCase()
-					+ ".sch";
-			InputStream baseIs = FhirValidator.class.getResourceAsStream(pathToBase);
-			try {
+				+ ".sch";
+			try (InputStream baseIs = FhirValidator.class.getResourceAsStream(pathToBase)) {
 				if (baseIs == null) {
 					throw new InternalErrorException("Failed to load schematron for resource '" + theCtx.getFhirContext().getResourceDefinition(theCtx.getResource()).getBaseDefinition().getName() + "'. "
-							+ SchemaBaseValidator.RESOURCES_JAR_NOTE);
+						+ SchemaBaseValidator.RESOURCES_JAR_NOTE);
 				}
-			} finally {
-				IOUtils.closeQuietly(baseIs);
+			} catch (IOException e) {
+				ourLog.error("Failed to close stream", e);
 			}
 
 			retVal = SchematronResourceSCH.fromClassPath(pathToBase);
@@ -143,5 +148,4 @@ public class SchematronBaseValidator implements IValidatorModule {
 			return retVal;
 		}
 	}
-
 }

hapi-fhir-base/src/test/java/ca/uhn/fhir/util/VersionEnumTest.java

@@ -0,0 +1,28 @@
+package ca.uhn.fhir.util;
+
+import org.junit.Test;
+
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import static org.hamcrest.CoreMatchers.hasItem;
+import static org.junit.Assert.assertThat;
+
+public class VersionEnumTest {
+
+	@Test
+	public void testCurrentVersionExists() {
+		List<String> versions = Arrays.stream(VersionEnum.values())
+			.map(Enum::name)
+			.collect(Collectors.toList());
+
+		String version = VersionUtil.getVersion();
+		version = "V" + version.replace(".", "_");
+		version = version.replace("-SNAPSHOT", "");
+
+		assertThat(versions, hasItem(version));
+	}
+
+
+}

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>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</version>
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
@@ -38,6 +38,11 @@
 			<artifactId>hapi-fhir-igpacks</artifactId>
 			<version>${project.version}</version>
 		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-jpaserver-migrate</artifactId>
+			<version>${project.version}</version>
+		</dependency>
 
 		<dependency>
 			<groupId>org.apache.commons</groupId>
@@ -83,6 +88,27 @@
 			<artifactId>commons-cli</artifactId>
 		</dependency>
 
+		<dependency>
+			<groupId>org.apache.derby</groupId>
+			<artifactId>derby</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.mariadb.jdbc</groupId>
+			<artifactId>mariadb-java-client</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>mysql</groupId>
+			<artifactId>mysql-connector-java</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.postgresql</groupId>
+			<artifactId>postgresql</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.microsoft.sqlserver</groupId>
+			<artifactId>mssql-jdbc</artifactId>
+		</dependency>
+
 		<dependency>
 			<groupId>org.springframework</groupId>
 			<artifactId>spring-core</artifactId>

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

@@ -27,7 +27,7 @@ import ch.qos.logback.core.joran.spi.JoranException;
 import com.helger.commons.io.file.FileHelper;
 import org.apache.commons.cli.*;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.lang3.text.WordUtils;
+import org.apache.commons.text.WordUtils;
 import org.fusesource.jansi.Ansi;
 import org.fusesource.jansi.AnsiConsole;
 import org.slf4j.LoggerFactory;
@@ -77,11 +77,6 @@ public abstract class BaseApp {
 	}
 
 	private void logCommandUsageNoHeader(BaseCommand theCommand) {
-		System.out.println("Usage:");
-		System.out.println("  " + provideCommandName() + " " + theCommand.getCommandName() + " [options]");
-		System.out.println();
-		System.out.println("Options:");
-
 		// This is passed in from the launch script
 		String columnsString = System.getProperty("columns");
 		int columns;
@@ -93,11 +88,34 @@ public abstract class BaseApp {
 			columns = 80;
 		}
 
+		// Usage
+		System.out.println("Usage:");
+		System.out.println("  " + provideCommandName() + " " + theCommand.getCommandName() + " [options]");
+		System.out.println();
+
+		// Description
+		String wrapped = WordUtils.wrap(theCommand.getCommandDescription(), columns);
+		System.out.println(wrapped);
+		System.out.println();
+
+		// Usage Notes
+		List<String> usageNotes = theCommand.provideUsageNotes();
+		for (String next : usageNotes) {
+			wrapped = WordUtils.wrap(next, columns);
+			System.out.println(wrapped);
+			System.out.println();
+		}
+
+		// Options
+		System.out.println("Options:");
 		HelpFormatter fmt = new HelpFormatter();
 		PrintWriter pw = new PrintWriter(System.out);
 		fmt.printOptions(pw, columns, theCommand.getOptions(), 2, 2);
 		pw.flush();
 		pw.close();
+
+		// That's it!
+		System.out.println();
 	}
 
 	private void logUsage() {
@@ -139,6 +157,7 @@ public abstract class BaseApp {
 		commands.add(new IgPackUploader());
 		commands.add(new ExportConceptMapToCsvCommand());
 		commands.add(new ImportCsvToConceptMapCommand());
+		commands.add(new HapiMigrateDatabaseCommand());
 		return commands;
 	}
 

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.cli;
  * 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.
@@ -36,7 +36,6 @@ import org.apache.http.client.methods.CloseableHttpResponse;
 import org.apache.http.client.methods.HttpGet;
 import org.apache.http.impl.client.CloseableHttpClient;
 import org.apache.http.impl.client.HttpClientBuilder;
-import org.fusesource.jansi.Ansi;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -52,6 +51,7 @@ import static org.apache.commons.lang3.StringUtils.*;
 import static org.fusesource.jansi.Ansi.ansi;
 
 public abstract class BaseCommand implements Comparable<BaseCommand> {
+	public static final String PROMPT = "PROMPT";
 	protected static final String BASE_URL_PARAM = "t";
 	protected static final String BASE_URL_PARAM_LONGOPT = "target";
 	protected static final String BASE_URL_PARAM_NAME = "target";
@@ -72,7 +72,6 @@ public abstract class BaseCommand implements Comparable<BaseCommand> {
 	protected static final String VERBOSE_LOGGING_PARAM_DESC = "If specified, verbose logging will be used.";
 	// TODO: Don't use qualified names for loggers in HAPI CLI.
 	private static final Logger ourLog = LoggerFactory.getLogger(BaseCommand.class);
-	public static final String PROMPT = "PROMPT";
 	protected FhirContext myFhirCtx;
 
 	public BaseCommand() {
@@ -99,7 +98,7 @@ public abstract class BaseCommand implements Comparable<BaseCommand> {
 		try {
 			retVal = reader.readLine();
 		} catch (IOException e) {
-			throw new ParseException("Failed to read input from user: "+ e.toString());
+			throw new ParseException("Failed to read input from user: " + e.toString());
 		}
 
 		System.out.print(ansi().boldOff().fgDefault());
@@ -117,7 +116,6 @@ public abstract class BaseCommand implements Comparable<BaseCommand> {
 	}
 
 
-
 	private void addOption(Options theOptions, OptionGroup theOptionGroup, boolean theRequired, String theOpt, String theLongOpt, boolean theHasArgument, String theArgumentName, String theDescription) {
 		Option option = createOption(theRequired, theOpt, theLongOpt, theHasArgument, theDescription);
 		if (theHasArgument && isNotBlank(theArgumentName)) {
@@ -268,9 +266,12 @@ public abstract class BaseCommand implements Comparable<BaseCommand> {
 		return basicAuthHeaderValue;
 	}
 
-	public <T extends Enum> T getAndParseOptionEnum(CommandLine theCommandLine, String theOption, Class<T> theEnumClass, T theDefault) throws ParseException {
+	public <T extends Enum> T getAndParseOptionEnum(CommandLine theCommandLine, String theOption, Class<T> theEnumClass, boolean theRequired, T theDefault) throws ParseException {
 		String val = theCommandLine.getOptionValue(theOption);
 		if (isBlank(val)) {
+			if (theRequired && theDefault == null) {
+				throw new ParseException("Missing required option -" + theOption);
+			}
 			return theDefault;
 		}
 		try {
@@ -329,7 +330,7 @@ public abstract class BaseCommand implements Comparable<BaseCommand> {
 			File suppliedFile = new File(FilenameUtils.normalize(theFilepath));
 
 			if (suppliedFile.isDirectory()) {
-				inputFiles = FileUtils.listFiles(suppliedFile, new String[] {"zip"}, false);
+				inputFiles = FileUtils.listFiles(suppliedFile, new String[]{"zip"}, false);
 			} else {
 				inputFiles = Collections.singletonList(suppliedFile);
 			}
@@ -433,4 +434,8 @@ public abstract class BaseCommand implements Comparable<BaseCommand> {
 
 
 	public abstract void run(CommandLine theCommandLine) throws ParseException, ExecutionException;
+
+	public List<String> provideUsageNotes() {
+		return Collections.emptyList();
+	}
 }

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

@@ -0,0 +1,98 @@
+package ca.uhn.fhir.cli;
+
+import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
+import ca.uhn.fhir.jpa.migrate.Migrator;
+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.Collections;
+import java.util.List;
+import java.util.stream.Collectors;
+
+public abstract class BaseMigrateDatabaseCommand<T extends Enum> extends BaseCommand {
+
+	private static final String MIGRATE_DATABASE = "migrate-database";
+
+	@Override
+	public String getCommandDescription() {
+		return "This command migrates a HAPI FHIR JPA database from one version of HAPI FHIR to a newer version";
+	}
+
+	protected abstract List<T> provideAllowedVersions();
+
+	protected abstract Class<T> provideVersionEnumType();
+
+	@Override
+	public String getCommandName() {
+		return MIGRATE_DATABASE;
+	}
+
+	@Override
+	public List<String> provideUsageNotes() {
+		String versions = "The following versions are supported: " +
+			provideAllowedVersions().stream().map(Enum::name).collect(Collectors.joining(", "));
+		return Collections.singletonList(versions);
+	}
+
+	@Override
+	public Options getOptions() {
+		Options retVal = new Options();
+
+		addOptionalOption(retVal, "r", "dry-run", false, "Log the SQL statements that would be executed but to not actually make any changes");
+
+		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, "f", "from", "Version", "The database schema version to migrate FROM");
+		addRequiredOption(retVal, "t", "to", "Version", "The database schema version to migrate TO");
+		addRequiredOption(retVal, "d", "driver", "Driver", "The database driver to use (Options are " + driverOptions() + ")");
+
+		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");
+		DriverTypeEnum driverType;
+		String driverTypeString = theCommandLine.getOptionValue("d");
+		try {
+			driverType = DriverTypeEnum.valueOf(driverTypeString);
+		} catch (Exception e) {
+			throw new ParseException("Invalid driver type \"" + driverTypeString + "\". Valid values are: " + driverOptions());
+		}
+
+		T from = getAndParseOptionEnum(theCommandLine, "f", provideVersionEnumType(), true, null);
+		validateVersionSupported(from);
+		T to = getAndParseOptionEnum(theCommandLine, "t", provideVersionEnumType(), true, null);
+		validateVersionSupported(to);
+
+		boolean dryRun = theCommandLine.hasOption("r");
+
+		Migrator migrator = new Migrator();
+		migrator.setConnectionUrl(url);
+		migrator.setDriverType(driverType);
+		migrator.setUsername(username);
+		migrator.setPassword(password);
+		migrator.setDryRun(dryRun);
+		addTasks(migrator, from, to);
+
+		migrator.migrate();
+	}
+
+	private void validateVersionSupported(T theFrom) throws ParseException {
+		if (provideAllowedVersions().contains(theFrom) == false) {
+			throw new ParseException("The version " + theFrom + " is not supported for migration");
+		}
+	}
+
+	protected abstract void addTasks(Migrator theMigrator, T theFrom, T theTo);
+}

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

@@ -0,0 +1,28 @@
+package ca.uhn.fhir.cli;
+
+import ca.uhn.fhir.jpa.migrate.Migrator;
+import ca.uhn.fhir.jpa.migrate.taskdef.BaseTask;
+import ca.uhn.fhir.jpa.migrate.tasks.HapiFhirJpaMigrationTasks;
+import ca.uhn.fhir.util.VersionEnum;
+
+import java.util.Arrays;
+import java.util.List;
+
+public class HapiMigrateDatabaseCommand extends BaseMigrateDatabaseCommand<VersionEnum> {
+
+	@Override
+	protected List<VersionEnum> provideAllowedVersions() {
+		return Arrays.asList(VersionEnum.values());
+	}
+
+	@Override
+	protected Class<VersionEnum> provideVersionEnumType() {
+		return VersionEnum.class;
+	}
+
+	@Override
+	protected void addTasks(Migrator theMigrator, VersionEnum theFrom, VersionEnum theTo) {
+		List<BaseTask<?>> tasks = new HapiFhirJpaMigrationTasks().getTasks(theFrom, theTo);
+		tasks.forEach(theMigrator::addTask);
+	}
+}

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

@@ -26,6 +26,7 @@ import ca.uhn.fhir.jpa.demo.FhirServerConfig;
 import ca.uhn.fhir.jpa.demo.FhirServerConfigDstu3;
 import ca.uhn.fhir.jpa.demo.FhirServerConfigR4;
 import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.OptionGroup;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.io.IOUtils;
@@ -71,6 +72,8 @@ public class RunServerCommand extends BaseCommand {
 		options.addOption(null, OPTION_ALLOW_EXTERNAL_REFS, false, "If this flag is set, the server will allow resources to be persisted contaning external resource references");
 		options.addOption(null, OPTION_DISABLE_REFERENTIAL_INTEGRITY, false, "If this flag is set, the server will not enforce referential integrity");
 
+		addOptionalOption(options, "u", "url", "Url", "If this option is set, specifies the JDBC URL to use for the database connection");
+
 		Long defaultReuseSearchResults = DaoConfig.DEFAULT_REUSE_CACHED_SEARCH_RESULTS_FOR_MILLIS;
 		String defaultReuseSearchResultsStr = defaultReuseSearchResults == null ? "off" : String.valueOf(defaultReuseSearchResults);
 		options.addOption(null, OPTION_REUSE_SEARCH_RESULTS_MILLIS, true, "The time in milliseconds within which the same results will be returned for multiple identical searches, or \"off\" (default is " + defaultReuseSearchResultsStr + ")");
@@ -106,6 +109,8 @@ public class RunServerCommand extends BaseCommand {
 			ContextHolder.setDisableReferentialIntegrity(true);
 		}
 
+		 ContextHolder.setDatabaseUrl(theCommandLine.getOptionValue("u"));
+
 		String reuseSearchResults = theCommandLine.getOptionValue(OPTION_REUSE_SEARCH_RESULTS_MILLIS);
 		if (reuseSearchResults != null) {
 			if (reuseSearchResults.equals("off")) {

hapi-fhir-cli/hapi-fhir-cli-api/src/main/resources/logback-cli-on.xml

@@ -38,6 +38,12 @@
 		<appender-ref ref="STDOUT" />
 	</logger>
 
+	<!--
+	Always log the migrator
+	-->
+	<logger name="ca.uhn.fhir.jpa.migrate" additivity="false" level="info">
+		<appender-ref ref="STDOUT" />
+	</logger>
 
 	<root level="warn">
 		<appender-ref ref="STDOUT" />

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

@@ -0,0 +1,93 @@
+package ca.uhn.fhir.cli;
+
+import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
+import com.google.common.base.Charsets;
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.IOUtils;
+import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import static org.apache.commons.lang3.StringUtils.isBlank;
+
+public class HapiMigrateDatabaseCommandTest {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(HapiMigrateDatabaseCommandTest.class);
+
+	static {
+		System.setProperty("test", "true");
+	}
+
+	@Test
+	public void testMigrate() throws IOException {
+
+		File directory = new File("target/migrator_derby_test_340_350");
+		if (directory.exists()) {
+			FileUtils.deleteDirectory(directory);
+		}
+
+		String url = "jdbc:derby:directory:target/migrator_derby_test_340_350;create=true";
+		DriverTypeEnum.ConnectionProperties connectionProperties = DriverTypeEnum.DERBY_EMBEDDED.newConnectionProperties(url, "", "");
+
+		String script = IOUtils.toString(HapiMigrateDatabaseCommandTest.class.getResourceAsStream("/persistence_create_derby107_340.sql"), 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);
+		}
+
+		connectionProperties.getTxTemplate().execute(t -> {
+			for (String next : scriptStatements) {
+				connectionProperties.newJdbcTemplate().execute(next);
+			}
+			return null;
+		});
+
+		ourLog.info("**********************************************");
+		ourLog.info("Done Setup, Starting Dry Run...");
+		ourLog.info("**********************************************");
+
+		String[] args = new String[]{
+			"migrate-database",
+			"-d", "DERBY_EMBEDDED",
+			"-u", url,
+			"-n", "",
+			"-p", "",
+			"-r",
+			"-f", "V3_4_0",
+			"-t", "V3_5_0"
+		};
+		App.main(args);
+
+		ourLog.info("**********************************************");
+		ourLog.info("Done Setup, Starting Migration...");
+		ourLog.info("**********************************************");
+
+		args = new String[]{
+			"migrate-database",
+			"-d", "DERBY_EMBEDDED",
+			"-u", url,
+			"-n", "",
+			"-p", "",
+			"-f", "V3_4_0",
+			"-t", "V3_5_0"
+		};
+		App.main(args);
+	}
+}

hapi-fhir-cli/hapi-fhir-cli-api/src/test/resources/persistence_create_derby107_340.sql

@@ -0,0 +1,156 @@
+create sequence SEQ_CNCPT_MAP_GRP_ELM_TGT_PID start with 1 increment by 50;
+create sequence SEQ_CODESYSTEM_PID start with 1 increment by 50;
+create sequence SEQ_CODESYSTEMVER_PID start with 1 increment by 50;
+create sequence SEQ_CONCEPT_DESIG_PID start with 1 increment by 50;
+create sequence SEQ_CONCEPT_MAP_GROUP_PID start with 1 increment by 50;
+create sequence SEQ_CONCEPT_MAP_GRP_ELM_PID start with 1 increment by 50;
+create sequence SEQ_CONCEPT_MAP_PID start with 1 increment by 50;
+create sequence SEQ_CONCEPT_PC_PID start with 1 increment by 50;
+create sequence SEQ_CONCEPT_PID start with 1 increment by 50;
+create sequence SEQ_CONCEPT_PROP_PID start with 1 increment by 50;
+create sequence SEQ_FORCEDID_ID start with 1 increment by 50;
+create sequence SEQ_HISTORYTAG_ID start with 1 increment by 50;
+create sequence SEQ_IDXCMPSTRUNIQ_ID start with 1 increment by 50;
+create sequence SEQ_RESLINK_ID start with 1 increment by 50;
+create sequence SEQ_RESOURCE_HISTORY_ID start with 1 increment by 50;
+create sequence SEQ_RESOURCE_ID start with 1 increment by 50;
+create sequence SEQ_RESPARMPRESENT_ID start with 1 increment by 50;
+create sequence SEQ_RESTAG_ID start with 1 increment by 50;
+create sequence SEQ_SEARCH start with 1 increment by 50;
+create sequence SEQ_SEARCH_INC start with 1 increment by 50;
+create sequence SEQ_SEARCH_RES start with 1 increment by 50;
+create sequence SEQ_SEARCHPARM_ID start with 1 increment by 50;
+create sequence SEQ_SPIDX_COORDS start with 1 increment by 50;
+create sequence SEQ_SPIDX_DATE start with 1 increment by 50;
+create sequence SEQ_SPIDX_NUMBER start with 1 increment by 50;
+create sequence SEQ_SPIDX_QUANTITY start with 1 increment by 50;
+create sequence SEQ_SPIDX_STRING start with 1 increment by 50;
+create sequence SEQ_SPIDX_TOKEN start with 1 increment by 50;
+create sequence SEQ_SPIDX_URI start with 1 increment by 50;
+create sequence SEQ_SUBSCRIPTION_ID start with 1 increment by 50;
+create sequence SEQ_TAGDEF_ID start with 1 increment by 50;
+create table HFJ_FORCED_ID (PID bigint not null, FORCED_ID varchar(100) not null, RESOURCE_PID bigint not null, RESOURCE_TYPE varchar(100) default '', primary key (PID));
+create table HFJ_HISTORY_TAG (PID bigint not null, TAG_ID bigint, RES_ID bigint not null, RES_TYPE varchar(30) not null, RES_VER_PID bigint not null, primary key (PID));
+create table HFJ_IDX_CMP_STRING_UNIQ (PID bigint not null, IDX_STRING varchar(150) not null, RES_ID bigint, primary key (PID));
+create table HFJ_RES_LINK (PID bigint not null, SRC_PATH varchar(100) not null, SRC_RESOURCE_ID bigint not null, SOURCE_RESOURCE_TYPE varchar(30) default '' not null, TARGET_RESOURCE_ID bigint, TARGET_RESOURCE_TYPE varchar(30) default '' not null, TARGET_RESOURCE_URL varchar(200), SP_UPDATED timestamp, primary key (PID));
+create table HFJ_RES_PARAM_PRESENT (PID bigint not null, SP_PRESENT boolean not null, RES_ID bigint not null, SP_ID bigint not null, primary key (PID));
+create table HFJ_RES_TAG (PID bigint not null, TAG_ID bigint, RES_ID bigint, RES_TYPE varchar(30) not null, primary key (PID));
+create table HFJ_RES_VER (PID bigint not null, RES_DELETED_AT timestamp, RES_VERSION varchar(7), HAS_TAGS boolean not null, RES_PUBLISHED timestamp not null, RES_UPDATED timestamp not null, RES_ENCODING varchar(5) not null, RES_TEXT blob, RES_ID bigint, RES_TYPE varchar(30) not null, RES_VER bigint not null, FORCED_ID_PID bigint, primary key (PID));
+create table HFJ_RESOURCE (RES_ID bigint not null, RES_DELETED_AT timestamp, RES_VERSION varchar(7), HAS_TAGS boolean not null, RES_PUBLISHED timestamp not null, RES_UPDATED timestamp not null, SP_HAS_LINKS boolean, HASH_SHA256 varchar(64), SP_INDEX_STATUS bigint, RES_LANGUAGE varchar(20), SP_CMPSTR_UNIQ_PRESENT boolean, SP_COORDS_PRESENT boolean, SP_DATE_PRESENT boolean, SP_NUMBER_PRESENT boolean, SP_QUANTITY_PRESENT boolean, SP_STRING_PRESENT boolean, SP_TOKEN_PRESENT boolean, SP_URI_PRESENT boolean, RES_PROFILE varchar(200), RES_TYPE varchar(30), RES_VER bigint, FORCED_ID_PID bigint, primary key (RES_ID));
+create table HFJ_SEARCH (PID bigint not null, CREATED timestamp not null, FAILURE_CODE integer, FAILURE_MESSAGE varchar(500), LAST_UPDATED_HIGH timestamp, LAST_UPDATED_LOW timestamp, NUM_FOUND integer not null, PREFERRED_PAGE_SIZE integer, RESOURCE_ID bigint, RESOURCE_TYPE varchar(200), SEARCH_LAST_RETURNED timestamp, SEARCH_QUERY_STRING clob(10000), SEARCH_QUERY_STRING_HASH integer, SEARCH_TYPE integer not null, SEARCH_STATUS varchar(10) not null, TOTAL_COUNT integer, SEARCH_UUID varchar(40) not null, primary key (PID));
+create table HFJ_SEARCH_INCLUDE (PID bigint not null, SEARCH_INCLUDE varchar(200) not null, INC_RECURSE boolean not null, REVINCLUDE boolean not null, SEARCH_PID bigint not null, primary key (PID));
+create table HFJ_SEARCH_PARM (PID bigint not null, PARAM_NAME varchar(100) not null, RES_TYPE varchar(30) not null, primary key (PID));
+create table HFJ_SEARCH_RESULT (PID bigint not null, SEARCH_ORDER integer not null, RESOURCE_PID bigint not null, SEARCH_PID bigint not null, primary key (PID));
+create table HFJ_SPIDX_COORDS (SP_ID bigint not null, SP_MISSING boolean, SP_NAME varchar(100) not null, RES_ID bigint, RES_TYPE varchar(255) not null, SP_UPDATED timestamp, SP_LATITUDE double, SP_LONGITUDE double, primary key (SP_ID));
+create table HFJ_SPIDX_DATE (SP_ID bigint not null, SP_MISSING boolean, SP_NAME varchar(100) not null, RES_ID bigint, RES_TYPE varchar(255) not null, SP_UPDATED timestamp, SP_VALUE_HIGH timestamp, SP_VALUE_LOW timestamp, primary key (SP_ID));
+create table HFJ_SPIDX_NUMBER (SP_ID bigint not null, SP_MISSING boolean, SP_NAME varchar(100) not null, RES_ID bigint, RES_TYPE varchar(255) not null, SP_UPDATED timestamp, SP_VALUE numeric(19,2), primary key (SP_ID));
+create table HFJ_SPIDX_QUANTITY (SP_ID bigint not null, SP_MISSING boolean, SP_NAME varchar(100) not null, RES_ID bigint, RES_TYPE varchar(255) not null, SP_UPDATED timestamp, HASH_UNITS_AND_VALPREFIX bigint, HASH_VALPREFIX bigint, SP_SYSTEM varchar(200), SP_UNITS varchar(200), SP_VALUE numeric(19,2), primary key (SP_ID));
+create table HFJ_SPIDX_STRING (SP_ID bigint not null, SP_MISSING boolean, SP_NAME varchar(100) not null, RES_ID bigint, RES_TYPE varchar(255) not null, SP_UPDATED timestamp, HASH_EXACT bigint, HASH_NORM_PREFIX bigint, SP_VALUE_EXACT varchar(200), SP_VALUE_NORMALIZED varchar(200), primary key (SP_ID));
+create table HFJ_SPIDX_TOKEN (SP_ID bigint not null, SP_MISSING boolean, SP_NAME varchar(100) not null, RES_ID bigint, RES_TYPE varchar(255) not null, SP_UPDATED timestamp, HASH_SYS bigint, HASH_SYS_AND_VALUE bigint, HASH_VALUE bigint, SP_SYSTEM varchar(200), SP_VALUE varchar(200), primary key (SP_ID));
+create table HFJ_SPIDX_URI (SP_ID bigint not null, SP_MISSING boolean, SP_NAME varchar(100) not null, RES_ID bigint, RES_TYPE varchar(255) not null, SP_UPDATED timestamp, HASH_URI bigint, SP_URI varchar(255), primary key (SP_ID));
+create table HFJ_SUBSCRIPTION_STATS (PID bigint not null, CREATED_TIME timestamp not null, RES_ID bigint, primary key (PID));
+create table HFJ_TAG_DEF (TAG_ID bigint not null, TAG_CODE varchar(200), TAG_DISPLAY varchar(200), TAG_SYSTEM varchar(200), TAG_TYPE integer not null, primary key (TAG_ID));
+create table TRM_CODESYSTEM (PID bigint not null, CODE_SYSTEM_URI varchar(255) not null, CS_NAME varchar(255), RES_ID bigint, CURRENT_VERSION_PID bigint, primary key (PID));
+create table TRM_CODESYSTEM_VER (PID bigint not null, CS_VERSION_ID varchar(255), CODESYSTEM_PID bigint, RES_ID bigint not null, primary key (PID));
+create table TRM_CONCEPT (PID bigint not null, CODE varchar(100) not null, CODESYSTEM_PID bigint, DISPLAY varchar(400), INDEX_STATUS bigint, CODE_SEQUENCE integer, primary key (PID));
+create table TRM_CONCEPT_DESIG (PID bigint not null, LANG varchar(500), USE_CODE varchar(500), USE_DISPLAY varchar(500), USE_SYSTEM varchar(500), VAL varchar(500) not null, CONCEPT_PID bigint, primary key (PID));
+create table TRM_CONCEPT_MAP (PID bigint not null, RES_ID bigint, SOURCE_URL varchar(200), TARGET_URL varchar(200), URL varchar(200) not null, primary key (PID));
+create table TRM_CONCEPT_MAP_GROUP (PID bigint not null, myConceptMapUrl varchar(255), SOURCE_URL varchar(200) not null, mySourceValueSet varchar(255), SOURCE_VERSION varchar(100), TARGET_URL varchar(200) not null, myTargetValueSet varchar(255), TARGET_VERSION varchar(100), CONCEPT_MAP_PID bigint not null, primary key (PID));
+create table TRM_CONCEPT_MAP_GRP_ELEMENT (PID bigint not null, SOURCE_CODE varchar(100) not null, myConceptMapUrl varchar(255), SOURCE_DISPLAY varchar(400), mySystem varchar(255), mySystemVersion varchar(255), myValueSet varchar(255), CONCEPT_MAP_GROUP_PID bigint not null, primary key (PID));
+create table TRM_CONCEPT_MAP_GRP_ELM_TGT (PID bigint not null, TARGET_CODE varchar(50) not null, myConceptMapUrl varchar(255), TARGET_DISPLAY varchar(400), TARGET_EQUIVALENCE varchar(50), mySystem varchar(255), mySystemVersion varchar(255), myValueSet varchar(255), CONCEPT_MAP_GRP_ELM_PID bigint not null, primary key (PID));
+create table TRM_CONCEPT_PC_LINK (PID bigint not null, CHILD_PID bigint, PARENT_PID bigint, REL_TYPE integer, CODESYSTEM_PID bigint not null, primary key (PID));
+create table TRM_CONCEPT_PROPERTY (PID bigint not null, PROP_CODESYSTEM varchar(500), PROP_DISPLAY varchar(500), PROP_KEY varchar(500) not null, PROP_TYPE integer not null, PROP_VAL varchar(500), CONCEPT_PID bigint, primary key (PID));
+create index IDX_FORCEDID_TYPE_FORCEDID on HFJ_FORCED_ID (RESOURCE_TYPE, FORCED_ID);
+create unique index IDX_FORCEDID_RESID on HFJ_FORCED_ID (RESOURCE_PID);
+create unique index IDX_FORCEDID_TYPE_RESID on HFJ_FORCED_ID (RESOURCE_TYPE, RESOURCE_PID);
+create unique index IDX_RESHISTTAG_TAGID on HFJ_HISTORY_TAG (RES_VER_PID, TAG_ID);
+create index IDX_IDXCMPSTRUNIQ_RESOURCE on HFJ_IDX_CMP_STRING_UNIQ (RES_ID);
+create unique index IDX_IDXCMPSTRUNIQ_STRING on HFJ_IDX_CMP_STRING_UNIQ (IDX_STRING);
+create index IDX_RL_TPATHRES on HFJ_RES_LINK (SRC_PATH, TARGET_RESOURCE_ID);
+create index IDX_RL_SRC on HFJ_RES_LINK (SRC_RESOURCE_ID);
+create index IDX_RL_DEST on HFJ_RES_LINK (TARGET_RESOURCE_ID);
+create index IDX_RESPARMPRESENT_RESID on HFJ_RES_PARAM_PRESENT (RES_ID);
+create unique index IDX_RESPARMPRESENT_SPID_RESID on HFJ_RES_PARAM_PRESENT (SP_ID, RES_ID);
+create unique index IDX_RESTAG_TAGID on HFJ_RES_TAG (RES_ID, TAG_ID);
+create index IDX_RESVER_TYPE_DATE on HFJ_RES_VER (RES_TYPE, RES_UPDATED);
+create index IDX_RESVER_ID_DATE on HFJ_RES_VER (RES_ID, RES_UPDATED);
+create index IDX_RESVER_DATE on HFJ_RES_VER (RES_UPDATED);
+create unique index IDX_RESVER_ID_VER on HFJ_RES_VER (RES_ID, RES_VER);
+create index IDX_RES_DATE on HFJ_RESOURCE (RES_UPDATED);
+create index IDX_RES_LANG on HFJ_RESOURCE (RES_TYPE, RES_LANGUAGE);
+create index IDX_RES_PROFILE on HFJ_RESOURCE (RES_PROFILE);
+create index IDX_RES_TYPE on HFJ_RESOURCE (RES_TYPE);
+create index IDX_INDEXSTATUS on HFJ_RESOURCE (SP_INDEX_STATUS);
+create index IDX_SEARCH_LASTRETURNED on HFJ_SEARCH (SEARCH_LAST_RETURNED);
+create index IDX_SEARCH_RESTYPE_HASHS on HFJ_SEARCH (RESOURCE_TYPE, SEARCH_QUERY_STRING_HASH, CREATED);
+create unique index IDX_SEARCH_UUID on HFJ_SEARCH (SEARCH_UUID);
+create unique index IDX_SEARCHPARM_RESTYPE_SPNAME on HFJ_SEARCH_PARM (RES_TYPE, PARAM_NAME);
+create unique index IDX_SEARCHRES_ORDER on HFJ_SEARCH_RESULT (SEARCH_PID, SEARCH_ORDER);
+create index IDX_SP_COORDS on HFJ_SPIDX_COORDS (RES_TYPE, SP_NAME, SP_LATITUDE, SP_LONGITUDE);
+create index IDX_SP_COORDS_UPDATED on HFJ_SPIDX_COORDS (SP_UPDATED);
+create index IDX_SP_COORDS_RESID on HFJ_SPIDX_COORDS (RES_ID);
+create index IDX_SP_DATE on HFJ_SPIDX_DATE (RES_TYPE, SP_NAME, SP_VALUE_LOW, SP_VALUE_HIGH);
+create index IDX_SP_DATE_UPDATED on HFJ_SPIDX_DATE (SP_UPDATED);
+create index IDX_SP_DATE_RESID on HFJ_SPIDX_DATE (RES_ID);
+create index IDX_SP_NUMBER on HFJ_SPIDX_NUMBER (RES_TYPE, SP_NAME, SP_VALUE);
+create index IDX_SP_NUMBER_UPDATED on HFJ_SPIDX_NUMBER (SP_UPDATED);
+create index IDX_SP_NUMBER_RESID on HFJ_SPIDX_NUMBER (RES_ID);
+create index IDX_SP_QUANTITY on HFJ_SPIDX_QUANTITY (RES_TYPE, SP_NAME, SP_SYSTEM, SP_UNITS, SP_VALUE);
+create index IDX_SP_QUANTITY_UPDATED on HFJ_SPIDX_QUANTITY (SP_UPDATED);
+create index IDX_SP_QUANTITY_RESID on HFJ_SPIDX_QUANTITY (RES_ID);
+create index IDX_SP_STRING on HFJ_SPIDX_STRING (RES_TYPE, SP_NAME, SP_VALUE_NORMALIZED);
+create index IDX_SP_STRING_UPDATED on HFJ_SPIDX_STRING (SP_UPDATED);
+create index IDX_SP_STRING_RESID on HFJ_SPIDX_STRING (RES_ID);
+create index IDX_SP_TOKEN on HFJ_SPIDX_TOKEN (RES_TYPE, SP_NAME, SP_SYSTEM, SP_VALUE);
+create index IDX_SP_TOKEN_UNQUAL on HFJ_SPIDX_TOKEN (RES_TYPE, SP_NAME, SP_VALUE);
+create index IDX_SP_TOKEN_UPDATED on HFJ_SPIDX_TOKEN (SP_UPDATED);
+create index IDX_SP_TOKEN_RESID on HFJ_SPIDX_TOKEN (RES_ID);
+create index IDX_SP_URI on HFJ_SPIDX_URI (RES_TYPE, SP_NAME, SP_URI);
+create index IDX_SP_URI_RESTYPE_NAME on HFJ_SPIDX_URI (RES_TYPE, SP_NAME);
+create index IDX_SP_URI_UPDATED on HFJ_SPIDX_URI (SP_UPDATED);
+create index IDX_SP_URI_COORDS on HFJ_SPIDX_URI (RES_ID);
+create unique index IDX_SUBSC_RESID on HFJ_SUBSCRIPTION_STATS (RES_ID);
+create unique index IDX_TAGDEF_TYPESYSCODE on HFJ_TAG_DEF (TAG_TYPE, TAG_SYSTEM, TAG_CODE);
+create unique index IDX_CS_CODESYSTEM on TRM_CODESYSTEM (CODE_SYSTEM_URI);
+create index IDX_CONCEPT_INDEXSTATUS on TRM_CONCEPT (INDEX_STATUS);
+create unique index IDX_CONCEPT_CS_CODE on TRM_CONCEPT (CODESYSTEM_PID, CODE);
+create unique index IDX_CONCEPT_MAP_URL on TRM_CONCEPT_MAP (URL);
+create index IDX_CNCPT_MAP_GRP_CD on TRM_CONCEPT_MAP_GRP_ELEMENT (SOURCE_CODE);
+create index IDX_CNCPT_MP_GRP_ELM_TGT_CD on TRM_CONCEPT_MAP_GRP_ELM_TGT (TARGET_CODE);
+alter table HFJ_FORCED_ID add constraint FK_FORCEDID_RESOURCE foreign key (RESOURCE_PID) references HFJ_RESOURCE;
+alter table HFJ_HISTORY_TAG add constraint FKtderym7awj6q8iq5c51xv4ndw foreign key (TAG_ID) references HFJ_TAG_DEF;
+alter table HFJ_HISTORY_TAG add constraint FK_HISTORYTAG_HISTORY foreign key (RES_VER_PID) references HFJ_RES_VER;
+alter table HFJ_IDX_CMP_STRING_UNIQ add constraint FK_IDXCMPSTRUNIQ_RES_ID foreign key (RES_ID) references HFJ_RESOURCE;
+alter table HFJ_RES_LINK add constraint FK_RESLINK_SOURCE foreign key (SRC_RESOURCE_ID) references HFJ_RESOURCE;
+alter table HFJ_RES_LINK add constraint FK_RESLINK_TARGET foreign key (TARGET_RESOURCE_ID) references HFJ_RESOURCE;
+alter table HFJ_RES_PARAM_PRESENT add constraint FK_RESPARMPRES_RESID foreign key (RES_ID) references HFJ_RESOURCE;
+alter table HFJ_RES_PARAM_PRESENT add constraint FK_RESPARMPRES_SPID foreign key (SP_ID) references HFJ_SEARCH_PARM;
+alter table HFJ_RES_TAG add constraint FKbfcjbaftmiwr3rxkwsy23vneo foreign key (TAG_ID) references HFJ_TAG_DEF;
+alter table HFJ_RES_TAG add constraint FK_RESTAG_RESOURCE foreign key (RES_ID) references HFJ_RESOURCE;
+alter table HFJ_RES_VER add constraint FKh20i7lcbchkaxekvwg9ix4hc5 foreign key (FORCED_ID_PID) references HFJ_FORCED_ID;
+alter table HFJ_RESOURCE add constraint FKhjgj8cp879gfxko25cx5o692r foreign key (FORCED_ID_PID) references HFJ_FORCED_ID;
+alter table HFJ_SEARCH_INCLUDE add constraint FK_SEARCHINC_SEARCH foreign key (SEARCH_PID) references HFJ_SEARCH;
+alter table HFJ_SEARCH_RESULT add constraint FK_SEARCHRES_RES foreign key (RESOURCE_PID) references HFJ_RESOURCE;
+alter table HFJ_SEARCH_RESULT add constraint FK_SEARCHRES_SEARCH foreign key (SEARCH_PID) references HFJ_SEARCH;
+alter table HFJ_SPIDX_COORDS add constraint FKc97mpk37okwu8qvtceg2nh9vn foreign key (RES_ID) references HFJ_RESOURCE;
+alter table HFJ_SPIDX_DATE add constraint FK17s70oa59rm9n61k9thjqrsqm foreign key (RES_ID) references HFJ_RESOURCE;
+alter table HFJ_SPIDX_NUMBER add constraint FKcltihnc5tgprj9bhpt7xi5otb foreign key (RES_ID) references HFJ_RESOURCE;
+alter table HFJ_SPIDX_QUANTITY add constraint FKn603wjjoi1a6asewxbbd78bi5 foreign key (RES_ID) references HFJ_RESOURCE;
+alter table HFJ_SPIDX_STRING add constraint FK_SPIDXSTR_RESOURCE foreign key (RES_ID) references HFJ_RESOURCE;
+alter table HFJ_SPIDX_TOKEN add constraint FK7ulx3j1gg3v7maqrejgc7ybc4 foreign key (RES_ID) references HFJ_RESOURCE;
+alter table HFJ_SPIDX_URI add constraint FKgxsreutymmfjuwdswv3y887do foreign key (RES_ID) references HFJ_RESOURCE;
+alter table HFJ_SUBSCRIPTION_STATS add constraint FK_SUBSC_RESOURCE_ID foreign key (RES_ID) references HFJ_RESOURCE;
+alter table TRM_CODESYSTEM add constraint FK_TRMCODESYSTEM_CURVER foreign key (CURRENT_VERSION_PID) references TRM_CODESYSTEM_VER;
+alter table TRM_CODESYSTEM add constraint FK_TRMCODESYSTEM_RES foreign key (RES_ID) references HFJ_RESOURCE;
+alter table TRM_CODESYSTEM_VER add constraint FK_CODESYSVER_CS_ID foreign key (CODESYSTEM_PID) references TRM_CODESYSTEM;
+alter table TRM_CODESYSTEM_VER add constraint FK_CODESYSVER_RES_ID foreign key (RES_ID) references HFJ_RESOURCE;
+alter table TRM_CONCEPT add constraint FK_CONCEPT_PID_CS_PID foreign key (CODESYSTEM_PID) references TRM_CODESYSTEM_VER;
+alter table TRM_CONCEPT_DESIG add constraint FK_CONCEPTDESIG_CONCEPT foreign key (CONCEPT_PID) references TRM_CONCEPT;
+alter table TRM_CONCEPT_MAP add constraint FK_TRMCONCEPTMAP_RES foreign key (RES_ID) references HFJ_RESOURCE;
+alter table TRM_CONCEPT_MAP_GROUP add constraint FK_TCMGROUP_CONCEPTMAP foreign key (CONCEPT_MAP_PID) references TRM_CONCEPT_MAP;
+alter table TRM_CONCEPT_MAP_GRP_ELEMENT add constraint FK_TCMGELEMENT_GROUP foreign key (CONCEPT_MAP_GROUP_PID) references TRM_CONCEPT_MAP_GROUP;
+alter table TRM_CONCEPT_MAP_GRP_ELM_TGT add constraint FK_TCMGETARGET_ELEMENT foreign key (CONCEPT_MAP_GRP_ELM_PID) references TRM_CONCEPT_MAP_GRP_ELEMENT;
+alter table TRM_CONCEPT_PC_LINK add constraint FK_TERM_CONCEPTPC_CHILD foreign key (CHILD_PID) references TRM_CONCEPT;
+alter table TRM_CONCEPT_PC_LINK add constraint FK_TERM_CONCEPTPC_CS foreign key (CODESYSTEM_PID) references TRM_CODESYSTEM_VER;
+alter table TRM_CONCEPT_PC_LINK add constraint FK_TERM_CONCEPTPC_PARENT foreign key (PARENT_PID) references TRM_CONCEPT;
+alter table TRM_CONCEPT_PROPERTY add constraint FK_CONCEPTPROP_CONCEPT foreign key (CONCEPT_PID) references TRM_CONCEPT;

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>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</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-fhir-cli</artifactId>
-		<version>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/ContextHolder.java

@@ -12,6 +12,7 @@ public class ContextHolder {
 	private static boolean ourDisableReferentialIntegrity;
 	private static String ourPath;
 	private static Long ourReuseSearchResultsMillis;
+	private static String ourDatabaseUrl;
 
 	static {
 		ourReuseSearchResultsMillis = DaoConfig.DEFAULT_REUSE_CACHED_SEARCH_RESULTS_FOR_MILLIS;
@@ -27,12 +28,15 @@ public class ContextHolder {
 			case DSTU2:
 				ourPath = "/baseDstu2/";
 				break;
+			case DSTU2_1:
+				break;
 			case DSTU3:
 				ourPath = "/baseDstu3/";
 				break;
 			case R4:
 				ourPath = "/baseR4/";
 				break;
+			case DSTU2_HL7ORG:
 			default:
 				throw new ParseException("FHIR version not supported by this command: " + theCtx.getVersion().getVersion());
 		}
@@ -68,4 +72,12 @@ public class ContextHolder {
 	public static void setDisableReferentialIntegrity(boolean theDisableReferentialIntegrity) {
 		ourDisableReferentialIntegrity = theDisableReferentialIntegrity;
 	}
+
+	public static String getDatabaseUrl() {
+		return ourDatabaseUrl;
+	}
+
+	public static void setDatabaseUrl(String theDatabaseUrl) {
+		ourDatabaseUrl = theDatabaseUrl;
+	}
 }

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirDbConfig.java

@@ -4,14 +4,38 @@ import java.util.Properties;
 
 import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
 import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
+import org.apache.commons.dbcp2.BasicDataSource;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 
+import javax.sql.DataSource;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
+@SuppressWarnings("Duplicates")
 @Configuration
 public class FhirDbConfig {
 
-	
-	private boolean ourLowMemMode;
+	/**
+	 * The following bean configures the database connection. The 'url' property value of "jdbc:derby:directory:jpaserver_derby_files;create=true" indicates that the server should save resources in a
+	 * directory called "jpaserver_derby_files".
+	 *
+	 * A URL to a remote database could also be placed here, along with login credentials and other properties supported by BasicDataSource.
+	 */
+	@Bean(destroyMethod = "close")
+	public DataSource dataSource() {
+		String url = "jdbc:derby:directory:target/jpaserver_derby_files;create=true";
+		if (isNotBlank(ContextHolder.getDatabaseUrl())) {
+			url = ContextHolder.getDatabaseUrl();
+		}
+
+		BasicDataSource retVal = new BasicDataSource();
+		retVal.setDriver(new org.apache.derby.jdbc.EmbeddedDriver());
+		retVal.setUrl(url);
+		retVal.setUsername("");
+		retVal.setPassword("");
+		return retVal;
+	}
 
 	@Bean()
 	public Properties jpaProperties() {

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfig.java

@@ -1,11 +1,11 @@
 package ca.uhn.fhir.jpa.demo;
 
-import java.util.Properties;
-
-import javax.persistence.EntityManagerFactory;
-import javax.sql.DataSource;
-
-import org.apache.commons.dbcp2.BasicDataSource;
+import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu2;
+import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
 import org.apache.commons.lang3.time.DateUtils;
 import org.hibernate.jpa.HibernatePersistenceProvider;
 import org.springframework.beans.factory.annotation.Autowire;
@@ -18,18 +18,21 @@ import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
 
-import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2;
-import ca.uhn.fhir.jpa.dao.DaoConfig;
-import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu2;
-import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
-import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
-import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
+import javax.persistence.EntityManagerFactory;
+import javax.sql.DataSource;
+import java.util.Properties;
 
 @Configuration
 @EnableTransactionManagement()
 @Import(FhirDbConfig.class)
 public class FhirServerConfig extends BaseJavaConfigDstu2 {
 
+	@Autowired
+	private DataSource myDataSource;
+	@Autowired()
+	@Qualifier("jpaProperties")
+	private Properties myJpaProperties;
+
 	/**
 	 * Configure FHIR properties around the the JPA server via this bean
 	 */
@@ -43,32 +46,12 @@ public class FhirServerConfig extends BaseJavaConfigDstu2 {
 		return retVal;
 	}
 
-	/**
-	 * The following bean configures the database connection. The 'url' property value of "jdbc:derby:directory:jpaserver_derby_files;create=true" indicates that the server should save resources in a
-	 * directory called "jpaserver_derby_files".
-	 * 
-	 * A URL to a remote database could also be placed here, along with login credentials and other properties supported by BasicDataSource.
-	 */
-	@Bean(destroyMethod = "close")
-	public DataSource dataSource() {
-		BasicDataSource retVal = new BasicDataSource();
-		retVal.setDriver(new org.apache.derby.jdbc.EmbeddedDriver());
-		retVal.setUrl("jdbc:derby:directory:target/jpaserver_derby_files;create=true");
-		retVal.setUsername("");
-		retVal.setPassword("");
-		return retVal;
-	}
-
-	@Autowired()
-	@Qualifier("jpaProperties")
-	private Properties myJpaProperties;
-
 	@Override
 	@Bean()
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
 		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
 		retVal.setPersistenceUnitName("HAPI_PU");
-		retVal.setDataSource(dataSource());
+		retVal.setDataSource(myDataSource);
 		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
 		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
 		retVal.setJpaProperties(myJpaProperties);
@@ -83,7 +66,7 @@ public class FhirServerConfig extends BaseJavaConfigDstu2 {
 		LoggingInterceptor retVal = new LoggingInterceptor();
 		retVal.setLoggerName("fhirtest.access");
 		retVal.setMessageFormat(
-				"Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${operationName} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}] ResponseEncoding[${responseEncodingNoDefault}]");
+			"Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${operationName} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}] ResponseEncoding[${responseEncodingNoDefault}]");
 		retVal.setLogExceptions(true);
 		retVal.setErrorMessageFormat("ERROR - ${requestVerb} ${requestUrl}");
 		return retVal;

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfigDstu3.java

@@ -1,13 +1,12 @@
 package ca.uhn.fhir.jpa.demo;
 
-import java.util.Properties;
-
-import javax.persistence.EntityManagerFactory;
-import javax.sql.DataSource;
-
-import org.apache.commons.dbcp2.BasicDataSource;
+import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu3;
+import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
 import org.apache.commons.lang3.time.DateUtils;
-import org.hibernate.jpa.HibernatePersistenceProvider;
 import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
@@ -18,18 +17,15 @@ import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
 
-import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
-import ca.uhn.fhir.jpa.dao.DaoConfig;
-import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu3;
-import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
-import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
-import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
+import javax.persistence.EntityManagerFactory;
+import javax.sql.DataSource;
+import java.util.Properties;
 
 /**
- * This class isn't used by default by the example, but 
+ * This class isn't used by default by the example, but
  * you can use it as a config if you want to support DSTU3
  * instead of DSTU2 in your server.
- * 
+ * <p>
  * See https://github.com/jamesagnew/hapi-fhir/issues/278
  */
 @Configuration
@@ -37,6 +33,12 @@ import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
 @Import(FhirDbConfig.class)
 public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
 
+	@Autowired
+	private DataSource myDataSource;
+	@Autowired()
+	@Qualifier("jpaProperties")
+	private Properties myJpaProperties;
+
 	/**
 	 * Configure FHIR properties around the the JPA server via this bean
 	 */
@@ -50,36 +52,16 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
 		return retVal;
 	}
 
-	/**
-	 * The following bean configures the database connection. The 'url' property value of "jdbc:derby:directory:jpaserver_derby_files;create=true" indicates that the server should save resources in a
-	 * directory called "jpaserver_derby_files".
-	 * 
-	 * A URL to a remote database could also be placed here, along with login credentials and other properties supported by BasicDataSource.
-	 */
-	@Bean(destroyMethod = "close")
-	public DataSource dataSource() {
-		BasicDataSource retVal = new BasicDataSource();
-		retVal.setDriver(new org.apache.derby.jdbc.EmbeddedDriver());
-		retVal.setUrl("jdbc:derby:directory:target/jpaserver_derby_files;create=true");
-		retVal.setUsername("");
-		retVal.setPassword("");
-		return retVal;
-	}
-
 	@Override
 	@Bean()
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
 		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
 		retVal.setPersistenceUnitName("HAPI_PU");
-		retVal.setDataSource(dataSource());
+		retVal.setDataSource(myDataSource);
 		retVal.setJpaProperties(myJpaProperties);
 		return retVal;
 	}
 
-	@Autowired()
-	@Qualifier("jpaProperties")
-	private Properties myJpaProperties;
-	
 	/**
 	 * Do some fancy logging to create a nice access log that has details about each incoming request.
 	 */
@@ -87,7 +69,7 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
 		LoggingInterceptor retVal = new LoggingInterceptor();
 		retVal.setLoggerName("fhirtest.access");
 		retVal.setMessageFormat(
-				"Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${operationName} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}] ResponseEncoding[${responseEncodingNoDefault}]");
+			"Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${operationName} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}] ResponseEncoding[${responseEncodingNoDefault}]");
 		retVal.setLogExceptions(true);
 		retVal.setErrorMessageFormat("ERROR - ${requestVerb} ${requestUrl}");
 		return retVal;

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfigR4.java

@@ -1,13 +1,12 @@
 package ca.uhn.fhir.jpa.demo;
 
-import java.util.Properties;
-
-import javax.persistence.EntityManagerFactory;
-import javax.sql.DataSource;
-
-import org.apache.commons.dbcp2.BasicDataSource;
+import ca.uhn.fhir.jpa.config.BaseJavaConfigR4;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorR4;
+import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
 import org.apache.commons.lang3.time.DateUtils;
-import org.hibernate.jpa.HibernatePersistenceProvider;
 import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
@@ -18,18 +17,15 @@ import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
 
-import ca.uhn.fhir.jpa.config.BaseJavaConfigR4;
-import ca.uhn.fhir.jpa.dao.DaoConfig;
-import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorR4;
-import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
-import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
-import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
+import javax.persistence.EntityManagerFactory;
+import javax.sql.DataSource;
+import java.util.Properties;
 
 /**
- * This class isn't used by default by the example, but 
+ * This class isn't used by default by the example, but
  * you can use it as a config if you want to support DSTU3
  * instead of DSTU2 in your server.
- * 
+ * <p>
  * See https://github.com/jamesagnew/hapi-fhir/issues/278
  */
 @Configuration
@@ -37,6 +33,12 @@ import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
 @Import(FhirDbConfig.class)
 public class FhirServerConfigR4 extends BaseJavaConfigR4 {
 
+	@Autowired
+	private DataSource myDataSource;
+	@Autowired()
+	@Qualifier("jpaProperties")
+	private Properties myJpaProperties;
+
 	/**
 	 * Configure FHIR properties around the the JPA server via this bean
 	 */
@@ -50,36 +52,16 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 {
 		return retVal;
 	}
 
-	/**
-	 * The following bean configures the database connection. The 'url' property value of "jdbc:derby:directory:jpaserver_derby_files;create=true" indicates that the server should save resources in a
-	 * directory called "jpaserver_derby_files".
-	 * 
-	 * A URL to a remote database could also be placed here, along with login credentials and other properties supported by BasicDataSource.
-	 */
-	@Bean(destroyMethod = "close")
-	public DataSource dataSource() {
-		BasicDataSource retVal = new BasicDataSource();
-		retVal.setDriver(new org.apache.derby.jdbc.EmbeddedDriver());
-		retVal.setUrl("jdbc:derby:directory:target/jpaserver_derby_files;create=true");
-		retVal.setUsername("");
-		retVal.setPassword("");
-		return retVal;
-	}
-
 	@Override
 	@Bean()
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
 		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
 		retVal.setPersistenceUnitName("HAPI_PU");
-		retVal.setDataSource(dataSource());
+		retVal.setDataSource(myDataSource);
 		retVal.setJpaProperties(myJpaProperties);
 		return retVal;
 	}
 
-	@Autowired()
-	@Qualifier("jpaProperties")
-	private Properties myJpaProperties;
-	
 	/**
 	 * Do some fancy logging to create a nice access log that has details about each incoming request.
 	 */
@@ -87,7 +69,7 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 {
 		LoggingInterceptor retVal = new LoggingInterceptor();
 		retVal.setLoggerName("fhirtest.access");
 		retVal.setMessageFormat(
-				"Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${operationName} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}] ResponseEncoding[${responseEncodingNoDefault}]");
+			"Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${operationName} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}] ResponseEncoding[${responseEncodingNoDefault}]");
 		retVal.setLogExceptions(true);
 		retVal.setErrorMessageFormat("ERROR - ${requestVerb} ${requestUrl}");
 		return retVal;

hapi-fhir-cli/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</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>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</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>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</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>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
@@ -16,14 +16,14 @@
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-base</artifactId>
-			<version>3.5.0-SNAPSHOT</version>
+			<version>3.5.0</version>
 		</dependency>
 
 		<!-- Server -->
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-server</artifactId>
-			<version>3.5.0-SNAPSHOT</version>
+			<version>3.5.0</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
@@ -35,43 +35,43 @@
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-dstu2</artifactId>
-			<version>3.5.0-SNAPSHOT</version>
+			<version>3.5.0</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
-			<version>3.5.0-SNAPSHOT</version>
+			<version>3.5.0</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-dstu2.1</artifactId>
-			<version>3.5.0-SNAPSHOT</version>
+			<version>3.5.0</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-dstu3</artifactId>
-			<version>3.5.0-SNAPSHOT</version>
+			<version>3.5.0</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-r4</artifactId>
-			<version>3.5.0-SNAPSHOT</version>
+			<version>3.5.0</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
-			<version>3.5.0-SNAPSHOT</version>
+			<version>3.5.0</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
-			<version>3.5.0-SNAPSHOT</version>
+			<version>3.5.0</version>
 			<optional>true</optional>
 		</dependency>
 

hapi-fhir-dist/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-igpacks/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<artifactId>hapi-deployable-pom</artifactId>
 		<groupId>ca.uhn.hapi.fhir</groupId>
-		<version>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>

hapi-fhir-jacoco/pom.xml

@@ -11,7 +11,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</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>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jaxrsserver-example/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-base/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
@@ -236,7 +236,12 @@
 			<artifactId>commons-dbcp2</artifactId>
 			<scope>test</scope>
 		</dependency>
-		<!-- 
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<!--
 		<dependency>
 			<groupId>org.apache.tomcat</groupId>
 			<artifactId>tomcat-catalina</artifactId>
@@ -338,6 +343,10 @@
 					<groupId>org.jboss.spec.javax.transaction</groupId>
 					<artifactId>jboss-transaction-api_1.2_spec</artifactId>
 				</exclusion>
+				<exclusion>
+					<groupId>javax.activation</groupId>
+					<artifactId>activation</artifactId>
+				</exclusion>
 			</exclusions>
 		</dependency>
 		<dependency>
@@ -394,10 +403,11 @@
 				</exclusion>
 			</exclusions>
 		</dependency>
-		<dependency>
+		<!--		<dependency>
 			<groupId>com.sun.activation</groupId>
 			<artifactId>javax.activation</artifactId>
 		</dependency>
+		-->
 		<!--<dependency>
 			<groupId>javax.validation</groupId>
 			<artifactId>validation-api</artifactId>
@@ -563,10 +573,21 @@
 							<goal>create</goal>
 						</goals>
 						<configuration>
-							<dialect>org.hibernate.dialect.MySQL57InnoDBDialect</dialect>
+							<dialect>org.hibernate.dialect.MySQL57Dialect</dialect>
 							<outputFile>${project.build.directory}/classes/ca/uhn/hapi/fhir/jpa/docs/database/persistence_create_mysql57.sql</outputFile>	
 						</configuration>
 					</execution>
+					<execution>
+						<id>mariadb103</id>
+						<phase>process-classes</phase>
+						<goals>
+							<goal>create</goal>
+						</goals>
+						<configuration>
+							<dialect>org.hibernate.dialect.MariaDB103Dialect</dialect>
+							<outputFile>${project.build.directory}/classes/ca/uhn/hapi/fhir/jpa/docs/database/persistence_create_mariadb103.sql</outputFile>	
+						</configuration>
+					</execution>
 					<execution>
 						<id>oracle12c</id>
 						<phase>process-classes</phase>

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/BaseHasResource.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/BaseResourceIndexedSearchParam.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ForcedId.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/IBaseResourceEntity.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.
@@ -19,23 +19,34 @@ package ca.uhn.fhir.jpa.entity;
  * limitations under the License.
  * #L%
  */
-import java.util.Date;
 
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
 
+import java.util.Date;
+
 public interface IBaseResourceEntity {
 
 	Date getDeleted();
+
 	FhirVersionEnum getFhirVersion();
+
 	Long getId();
+
 	IdDt getIdDt();
+
 	InstantDt getPublished();
+
 	Long getResourceId();
+
 	String getResourceType();
+
 	InstantDt getUpdated();
+
 	Date getUpdatedDate();
+
 	long getVersion();
+
 	boolean isHasTags();
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceEncodingEnum.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.
@@ -34,10 +34,14 @@ public enum ResourceEncodingEnum {
 	 * See ResourceHistoryTable RES_ENCODING column
 	 */
 
-	/** Json */
+	/**
+	 * Json
+	 */
 	JSON,
-	
-	/** Json Compressed */
+
+	/**
+	 * Json Compressed
+	 */
 	JSONC,
 
 	/**
@@ -48,5 +52,5 @@ public enum ResourceEncodingEnum {
 	public IParser newParser(FhirContext theContext) {
 		return theContext.newJsonParser();
 	}
-	
+
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceHistoryTable.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceIndexedCompositeStringUnique.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceIndexedSearchParamCoords.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.
@@ -32,7 +32,7 @@ import javax.persistence.*;
 @Embeddable
 @Entity
 @Table(name = "HFJ_SPIDX_COORDS", indexes = {
-	@Index(name = "IDX_SP_COORDS", columnList = "RES_TYPE,SP_NAME,SP_LATITUDE,SP_LONGITUDE"),
+	@Index(name = "IDX_SP_COORDS_HASH", columnList = "HASH_IDENTITY,SP_LATITUDE,SP_LONGITUDE"),
 	@Index(name = "IDX_SP_COORDS_UPDATED", columnList = "SP_UPDATED"),
 	@Index(name = "IDX_SP_COORDS_RESID", columnList = "RES_ID")
 })

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceIndexedSearchParamDate.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.
@@ -37,7 +37,7 @@ import java.util.Date;
 @Embeddable
 @Entity
 @Table(name = "HFJ_SPIDX_DATE", indexes = {
-//	@Index(name = "IDX_SP_DATE", columnList = "RES_TYPE,SP_NAME,SP_VALUE_LOW,SP_VALUE_HIGH"),
+	// We previously had an index called IDX_SP_DATE - Dont reuse
 	@Index(name = "IDX_SP_DATE_HASH", columnList = "HASH_IDENTITY,SP_VALUE_LOW,SP_VALUE_HIGH"),
 	@Index(name = "IDX_SP_DATE_UPDATED", columnList = "SP_UPDATED"),
 	@Index(name = "IDX_SP_DATE_RESID", columnList = "RES_ID")

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceIndexedSearchParamNumber.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.
@@ -37,7 +37,7 @@ import java.math.BigDecimal;
 @Embeddable
 @Entity
 @Table(name = "HFJ_SPIDX_NUMBER", indexes = {
-//	@Index(name = "IDX_SP_NUMBER", columnList = "RES_TYPE,SP_NAME,SP_VALUE"),
+//	We used to have an index with name IDX_SP_NUMBER - Dont reuse
 	@Index(name = "IDX_SP_NUMBER_HASH_VAL", columnList = "HASH_IDENTITY,SP_VALUE"),
 	@Index(name = "IDX_SP_NUMBER_UPDATED", columnList = "SP_UPDATED"),
 	@Index(name = "IDX_SP_NUMBER_RESID", columnList = "RES_ID")

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceIndexedSearchParamQuantity.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.
@@ -38,13 +38,13 @@ import java.math.BigDecimal;
 @Embeddable
 @Entity
 @Table(name = "HFJ_SPIDX_QUANTITY", indexes = {
-//	@Index(name = "IDX_SP_QUANTITY", columnList = "RES_TYPE,SP_NAME,SP_SYSTEM,SP_UNITS,SP_VALUE"),
+//	We used to have an index named IDX_SP_QUANTITY - Dont reuse
 	@Index(name = "IDX_SP_QUANTITY_HASH", columnList = "HASH_IDENTITY,SP_VALUE"),
 	@Index(name = "IDX_SP_QUANTITY_HASH_UN", columnList = "HASH_IDENTITY_AND_UNITS,SP_VALUE"),
+	@Index(name = "IDX_SP_QUANTITY_HASH_SYSUN", columnList = "HASH_IDENTITY_SYS_UNITS,SP_VALUE"),
 	@Index(name = "IDX_SP_QUANTITY_UPDATED", columnList = "SP_UPDATED"),
 	@Index(name = "IDX_SP_QUANTITY_RESID", columnList = "RES_ID")
 })
-//@formatter:on
 public class ResourceIndexedSearchParamQuantity extends BaseResourceIndexedSearchParam {
 
 	private static final int MAX_LENGTH = 200;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceIndexedSearchParamString.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceIndexedSearchParamToken.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceIndexedSearchParamUri.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceLink.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.
@@ -20,36 +20,21 @@ package ca.uhn.fhir.jpa.entity;
  * #L%
  */
 
-import java.io.Serializable;
-import java.util.Date;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.ForeignKey;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.SequenceGenerator;
-import javax.persistence.Table;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
-
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
-import org.hibernate.annotations.ColumnDefault;
 import org.hibernate.search.annotations.Field;
 import org.hl7.fhir.instance.model.api.IIdType;
 
+import javax.persistence.*;
+import java.io.Serializable;
+import java.util.Date;
+
 @Entity
-@Table(name = "HFJ_RES_LINK" , indexes= {
-	@Index(name="IDX_RL_TPATHRES", columnList= "SRC_PATH,TARGET_RESOURCE_ID"), 
-	@Index(name="IDX_RL_SRC", columnList= "SRC_RESOURCE_ID"), 
-	@Index(name="IDX_RL_DEST", columnList= "TARGET_RESOURCE_ID")
+@Table(name = "HFJ_RES_LINK", indexes = {
+	@Index(name = "IDX_RL_TPATHRES", columnList = "SRC_PATH,TARGET_RESOURCE_ID"),
+	@Index(name = "IDX_RL_SRC", columnList = "SRC_RESOURCE_ID"),
+	@Index(name = "IDX_RL_DEST", columnList = "TARGET_RESOURCE_ID")
 })
 public class ResourceLink implements Serializable {
 
@@ -64,30 +49,30 @@ public class ResourceLink implements Serializable {
 	@Column(name = "SRC_PATH", length = 100, nullable = false)
 	private String mySourcePath;
 
-	@ManyToOne(optional = false, fetch=FetchType.LAZY)
-	@JoinColumn(name = "SRC_RESOURCE_ID", referencedColumnName = "RES_ID", nullable = false, foreignKey=@ForeignKey(name="FK_RESLINK_SOURCE"))
+	@ManyToOne(optional = false, fetch = FetchType.LAZY)
+	@JoinColumn(name = "SRC_RESOURCE_ID", referencedColumnName = "RES_ID", nullable = false, foreignKey = @ForeignKey(name = "FK_RESLINK_SOURCE"))
 	private ResourceTable mySourceResource;
 
 	@Column(name = "SRC_RESOURCE_ID", insertable = false, updatable = false, nullable = false)
 	private Long mySourceResourcePid;
 
-	@Column(name = "SOURCE_RESOURCE_TYPE", nullable=false, length=ResourceTable.RESTYPE_LEN)
+	@Column(name = "SOURCE_RESOURCE_TYPE", nullable = false, length = ResourceTable.RESTYPE_LEN)
 	@Field()
 	private String mySourceResourceType;
 
-	@ManyToOne(optional = true, fetch=FetchType.LAZY)
-	@JoinColumn(name = "TARGET_RESOURCE_ID", referencedColumnName = "RES_ID", nullable = true, foreignKey=@ForeignKey(name="FK_RESLINK_TARGET"))
+	@ManyToOne(optional = true, fetch = FetchType.LAZY)
+	@JoinColumn(name = "TARGET_RESOURCE_ID", referencedColumnName = "RES_ID", nullable = true, foreignKey = @ForeignKey(name = "FK_RESLINK_TARGET"))
 	private ResourceTable myTargetResource;
 
 	@Column(name = "TARGET_RESOURCE_ID", insertable = false, updatable = false, nullable = true)
 	@Field()
 	private Long myTargetResourcePid;
 
-	@Column(name = "TARGET_RESOURCE_TYPE", nullable=false, length=ResourceTable.RESTYPE_LEN)
+	@Column(name = "TARGET_RESOURCE_TYPE", nullable = false, length = ResourceTable.RESTYPE_LEN)
 	@Field()
 	private String myTargetResourceType;
 
-	@Column(name = "TARGET_RESOURCE_URL", length=200, nullable = true)
+	@Column(name = "TARGET_RESOURCE_URL", length = 200, nullable = true)
 	@Field()
 	private String myTargetResourceUrl;
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceSearchView.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.
@@ -19,44 +19,36 @@ package ca.uhn.fhir.jpa.entity;
  * limitations under the License.
  * #L%
  */
-import java.io.Serializable;
-import java.util.Date;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
-import javax.persistence.Id;
-import javax.persistence.Lob;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
-
-import org.hibernate.annotations.Immutable;
-import org.hibernate.annotations.Subselect;
 
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.rest.api.Constants;
+import org.hibernate.annotations.Immutable;
+import org.hibernate.annotations.Subselect;
+
+import javax.persistence.*;
+import java.io.Serializable;
+import java.util.Date;
 
 //@formatter:off
 @Entity
 @Immutable
-@Subselect("SELECT h.pid        as pid            " + 
-		",  h.res_id            as res_id         "	+ 
-		",  h.res_type          as res_type       " + 
-		",  h.res_version       as res_version    " + // FHIR version
-		",  h.res_ver           as res_ver        " + // resource version
-		",  h.has_tags          as has_tags       " + 
-		",  h.res_deleted_at    as res_deleted_at "	+ 
-		",  h.res_published     as res_published  " + 
-		",  h.res_updated       as res_updated    "	+ 
-		",  h.res_text          as res_text       " + 
-		",  h.res_encoding      as res_encoding   "	+ 
-		",  f.forced_id         as forced_pid      " + 
-		"FROM HFJ_RES_VER h "
-		+ "    LEFT OUTER JOIN HFJ_FORCED_ID f ON f.resource_pid = h.res_id "
-		+ "    INNER JOIN HFJ_RESOURCE r       ON r.res_id = h.res_id and r.res_ver = h.res_ver")
+@Subselect("SELECT h.pid        as pid            " +
+	",  h.res_id            as res_id         " +
+	",  h.res_type          as res_type       " +
+	",  h.res_version       as res_version    " + // FHIR version
+	",  h.res_ver           as res_ver        " + // resource version
+	",  h.has_tags          as has_tags       " +
+	",  h.res_deleted_at    as res_deleted_at " +
+	",  h.res_published     as res_published  " +
+	",  h.res_updated       as res_updated    " +
+	",  h.res_text          as res_text       " +
+	",  h.res_encoding      as res_encoding   " +
+	",  f.forced_id         as forced_pid      " +
+	"FROM HFJ_RES_VER h "
+	+ "    LEFT OUTER JOIN HFJ_FORCED_ID f ON f.resource_pid = h.res_id "
+	+ "    INNER JOIN HFJ_RESOURCE r       ON r.res_id = h.res_id and r.res_ver = h.res_ver")
 // @formatter:on
 public class ResourceSearchView implements IBaseResourceEntity, Serializable {
 
@@ -142,7 +134,7 @@ public class ResourceSearchView implements IBaseResourceEntity, Serializable {
 			return new IdDt(myResourceType + '/' + id + '/' + Constants.PARAM_HISTORY + '/' + getVersion());
 		} else {
 			return new IdDt(
-					getResourceType() + '/' + getForcedId() + '/' + Constants.PARAM_HISTORY + '/' + getVersion());
+				getResourceType() + '/' + getForcedId() + '/' + Constants.PARAM_HISTORY + '/' + getVersion());
 		}
 	}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/Search.java

@@ -19,9 +19,9 @@ import static org.apache.commons.lang3.StringUtils.left;
  * 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.

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/SearchParamPresent.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.
@@ -28,6 +28,7 @@ import java.io.Serializable;
 
 @Entity
 @Table(name = "HFJ_RES_PARAM_PRESENT", indexes = {
+	// We used to have a constraint named IDX_RESPARMPRESENT_SPID_RESID - Don't reuse
 	@Index(name = "IDX_RESPARMPRESENT_RESID", columnList = "RES_ID"),
 	@Index(name = "IDX_RESPARMPRESENT_HASHPRES", columnList = "HASH_PRESENCE")
 })

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java

@@ -29,9 +29,9 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
  * 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.
@@ -93,15 +93,17 @@ public class TermConcept implements Serializable {
 	private Long myIndexStatus;
 	@Field(name = "myParentPids", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "conceptParentPidsAnalyzer"))
 	@Lob
-	@Column(name="PARENT_PIDS", nullable = true)
+	@Column(name = "PARENT_PIDS", nullable = true)
 	private String myParentPids;
 	@OneToMany(cascade = {}, fetch = FetchType.LAZY, mappedBy = "myChild")
 	private Collection<TermConceptParentChildLink> myParents;
 	@Column(name = "CODE_SEQUENCE", nullable = true)
 	private Integer mySequence;
+
 	public TermConcept() {
 		super();
 	}
+
 	public TermConcept(TermCodeSystemVersion theCs, String theCode) {
 		setCodeSystemVersion(theCs);
 		setCode(theCode);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptDesignation.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptMap.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptMapGroup.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.
@@ -38,7 +38,7 @@ public class TermConceptMapGroup implements Serializable {
 	private Long myId;
 
 	@ManyToOne()
-	@JoinColumn(name = "CONCEPT_MAP_PID", nullable = false, referencedColumnName = "PID", foreignKey=@ForeignKey(name="FK_TCMGROUP_CONCEPTMAP"))
+	@JoinColumn(name = "CONCEPT_MAP_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TCMGROUP_CONCEPTMAP"))
 	private TermConceptMap myConceptMap;
 
 	@Column(name = "SOURCE_URL", nullable = false, length = 200)

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptMapGroupElement.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.
@@ -42,7 +42,7 @@ public class TermConceptMapGroupElement implements Serializable {
 	private Long myId;
 
 	@ManyToOne()
-	@JoinColumn(name = "CONCEPT_MAP_GROUP_PID", nullable = false, referencedColumnName = "PID", foreignKey=@ForeignKey(name="FK_TCMGELEMENT_GROUP"))
+	@JoinColumn(name = "CONCEPT_MAP_GROUP_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TCMGELEMENT_GROUP"))
 	private TermConceptMapGroup myConceptMapGroup;
 
 	@Column(name = "SOURCE_CODE", nullable = false, length = TermConcept.CODE_LENGTH)

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptMapGroupElementTarget.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.
@@ -41,7 +41,7 @@ public class TermConceptMapGroupElementTarget implements Serializable {
 	private Long myId;
 
 	@ManyToOne()
-	@JoinColumn(name = "CONCEPT_MAP_GRP_ELM_PID", nullable = false, referencedColumnName = "PID", foreignKey=@ForeignKey(name="FK_TCMGETARGET_ELEMENT"))
+	@JoinColumn(name = "CONCEPT_MAP_GRP_ELM_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TCMGETARGET_ELEMENT"))
 	private TermConceptMapGroupElement myConceptMapGroupElement;
 
 	@Column(name = "TARGET_CODE", nullable = false, length = TermConcept.CODE_LENGTH)

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptProperty.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptPropertyFieldBridge.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4Config.java

@@ -105,7 +105,7 @@ public class TestR4Config extends BaseJavaConfigR4 {
 
 		DataSource dataSource = ProxyDataSourceBuilder
 			.create(retVal)
-//			.logQueryBySlf4j(SLF4JLogLevel.INFO, "SQL")
+			.logQueryBySlf4j(SLF4JLogLevel.INFO, "SQL")
 			.logSlowQueryBySlf4j(10, TimeUnit.SECONDS)
 			.countQuery(new ThreadQueryCountHolder())
 			.build();

hapi-fhir-jpaserver-elasticsearch/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-example/pom.xml

@@ -10,7 +10,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-example/src/main/java/ca/uhn/fhir/jpa/demo/JpaServerDemo.java

@@ -3,6 +3,11 @@ package ca.uhn.fhir.jpa.demo;
 
 import java.util.Collection;
 import java.util.List;
+
+import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
+import ca.uhn.fhir.jpa.subscription.email.SubscriptionEmailInterceptor;
+import ca.uhn.fhir.jpa.subscription.resthook.SubscriptionRestHookInterceptor;
+import ca.uhn.fhir.jpa.subscription.websocket.SubscriptionWebsocketInterceptor;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -151,9 +156,15 @@ public class JpaServerDemo extends RestfulServer {
 		 * so it is a potential security vulnerability. Consider using an AuthorizationInterceptor
 		 * with this feature.
 		 */
-		//if (fhirVersion == FhirVersionEnum.DSTU3) {
-		//	 registerProvider(myAppCtx.getBean(TerminologyUploaderProviderDstu3.class));
-		//}
+		if (fhirVersion == FhirVersionEnum.DSTU3) {
+			 registerProvider(myAppCtx.getBean(TerminologyUploaderProviderDstu3.class));
+		}
+
+		// Enable various subscription types
+		registerInterceptor(myAppCtx.getBean(SubscriptionWebsocketInterceptor.class));
+		registerInterceptor(myAppCtx.getBean(SubscriptionRestHookInterceptor.class));
+		registerInterceptor(myAppCtx.getBean(SubscriptionEmailInterceptor.class));
+
 	}
 
 }

hapi-fhir-jpaserver-migrate/pom.xml

@@ -0,0 +1,153 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+
+	<parent>
+		<groupId>ca.uhn.hapi.fhir</groupId>
+		<artifactId>hapi-deployable-pom</artifactId>
+		<version>3.5.0</version>
+		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
+	</parent>
+
+	<artifactId>hapi-fhir-jpaserver-migrate</artifactId>
+	<packaging>jar</packaging>
+
+	<name>HAPI FHIR JPA Server - Migration</name>
+
+	<dependencies>
+		<dependency>
+			<groupId>mysql</groupId>
+			<artifactId>mysql-connector-java</artifactId>
+			<version>6.0.5</version>
+		</dependency>
+		<!--
+		<dependency>
+			<groupId>org.aspectj</groupId>
+			<artifactId>aspectjweaver</artifactId>
+			<version>1.8.9</version>
+		</dependency>
+		-->
+
+		<dependency>
+			<groupId>org.springframework</groupId>
+			<artifactId>spring-jdbc</artifactId>
+		</dependency>
+
+		<!-- This dependency includes the core HAPI-FHIR classes -->
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-jpaserver-base</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+
+		<!-- Test Database -->
+		<dependency>
+			<groupId>org.apache.derby</groupId>
+			<artifactId>derby</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-dbcp2</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>ch.qos.logback</groupId>
+			<artifactId>logback-classic</artifactId>
+			<scope>test</scope>
+		</dependency>
+
+		<dependency>
+			<groupId>com.intellij</groupId>
+			<artifactId>annotations</artifactId>
+			<version>12.0</version>
+		</dependency>
+
+	</dependencies>
+
+	<build>
+
+		<!-- Tells Maven to name the generated WAR file as hapi-fhir-jpaserver-example.war -->
+		<finalName>hapi-fhir-jpaserver-example</finalName>
+
+		<!-- The following is not required for the application to build, but allows you to test it by issuing "mvn jetty:run" from the command line. -->
+		<pluginManagement>
+			<plugins>
+				<plugin>
+					<groupId>org.eclipse.jetty</groupId>
+					<artifactId>jetty-maven-plugin</artifactId>
+					<configuration>
+						<webApp>
+							<contextPath>/hapi-fhir-jpaserver-example</contextPath>
+							<allowDuplicateFragmentNames>true</allowDuplicateFragmentNames>
+						</webApp>
+					</configuration>
+				</plugin>
+			</plugins>
+		</pluginManagement>
+
+		<plugins>
+			<!-- Tell Maven which Java source version you want to use -->
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-compiler-plugin</artifactId>
+				<configuration>
+					<source>8</source>
+					<target>8</target>
+				</configuration>
+			</plugin>
+
+			<!-- The configuration here tells the WAR plugin to include the FHIR Tester overlay. You can omit it if you are not using that feature. -->
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-war-plugin</artifactId>
+				<configuration>
+					<archive>
+						<manifestEntries>
+							<Build-Time>${maven.build.timestamp}</Build-Time>
+						</manifestEntries>
+					</archive>
+					<overlays>
+						<overlay>
+							<groupId>ca.uhn.hapi.fhir</groupId>
+							<artifactId>hapi-fhir-testpage-overlay</artifactId>
+						</overlay>
+					</overlays>
+					<webXml>src/main/webapp/WEB-INF/web.xml</webXml>
+				</configuration>
+			</plugin>
+
+			<!-- This plugin is just a part of the HAPI internal build process, you do not need to incude it in your own projects -->
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-deploy-plugin</artifactId>
+				<configuration>
+					<skip>true</skip>
+				</configuration>
+			</plugin>
+
+			<!-- This is to run the integration tests -->
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-failsafe-plugin</artifactId>
+				<configuration>
+					<redirectTestOutputToFile>true</redirectTestOutputToFile>
+				</configuration>
+				<executions>
+					<execution>
+						<goals>
+							<goal>integration-test</goal>
+							<goal>verify</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+
+		</plugins>
+	</build>
+
+</project>

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

@@ -0,0 +1,114 @@
+package ca.uhn.fhir.jpa.migrate;
+
+import org.apache.commons.lang3.Validate;
+import org.springframework.jdbc.core.JdbcTemplate;
+import org.springframework.jdbc.datasource.DataSourceTransactionManager;
+import org.springframework.jdbc.datasource.SingleConnectionDataSource;
+import org.springframework.transaction.TransactionDefinition;
+import org.springframework.transaction.support.TransactionTemplate;
+
+import javax.annotation.Nonnull;
+
+/*-
+ * #%L
+ * Smile CDR - CDR
+ * %%
+ * Copyright (C) 2016 - 2018 Simpatico Intelligent Systems Inc
+ * %%
+ * All rights reserved.
+ * #L%
+ */
+
+public enum DriverTypeEnum {
+
+	DERBY_EMBEDDED("org.apache.derby.jdbc.EmbeddedDriver", true),
+	MARIADB_10_1("org.mariadb.jdbc.Driver", false),
+
+	// Formerly com.mysql.jdbc.Driver
+	MYSQL_5_7("com.mysql.cj.jdbc.Driver", false),
+
+	POSTGRES_9_4("org.postgresql.Driver", false),
+
+	ORACLE_12C("oracle.jdbc.OracleDriver", false),
+
+	MSSQL_2012("com.microsoft.sqlserver.jdbc.SQLServerDataSource", false),
+
+	;
+
+	private String myDriverClassName;
+	private boolean myDerby;
+
+	/**
+	 * Constructor
+	 */
+	DriverTypeEnum(String theDriverClassName, boolean theDerby) {
+		myDriverClassName = theDriverClassName;
+		myDerby = theDerby;
+	}
+
+
+	public ConnectionProperties newConnectionProperties(String theUrl, String theUsername, String thePassword) {
+		SingleConnectionDataSource dataSource = new SingleConnectionDataSource();
+		dataSource.setAutoCommit(false);
+		dataSource.setDriverClassName(myDriverClassName);
+		dataSource.setUrl(theUrl);
+		dataSource.setUsername(theUsername);
+		dataSource.setPassword(thePassword);
+		dataSource.setSuppressClose(true);
+
+		DataSourceTransactionManager transactionManager = new DataSourceTransactionManager();
+		transactionManager.setDataSource(dataSource);
+		transactionManager.afterPropertiesSet();
+
+		TransactionTemplate txTemplate = new TransactionTemplate();
+		txTemplate.setTransactionManager(transactionManager);
+		txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
+		txTemplate.afterPropertiesSet();
+
+		return new ConnectionProperties(dataSource, txTemplate, this);
+	}
+
+	public static class ConnectionProperties {
+
+		private final DriverTypeEnum myDriverType;
+		private final SingleConnectionDataSource myDataSource;
+		private final TransactionTemplate myTxTemplate;
+		/**
+		 * Constructor
+		 */
+		public ConnectionProperties(SingleConnectionDataSource theDataSource, TransactionTemplate theTxTemplate, DriverTypeEnum theDriverType) {
+			Validate.notNull(theDataSource);
+			Validate.notNull(theTxTemplate);
+			Validate.notNull(theDriverType);
+
+			myDataSource = theDataSource;
+			myTxTemplate = theTxTemplate;
+			myDriverType = theDriverType;
+		}
+
+		public DriverTypeEnum getDriverType() {
+			return myDriverType;
+		}
+
+		@Nonnull
+		public SingleConnectionDataSource getDataSource() {
+			return myDataSource;
+		}
+
+		@Nonnull
+		public JdbcTemplate newJdbcTemplate() {
+			JdbcTemplate jdbcTemplate = new JdbcTemplate();
+			jdbcTemplate.setDataSource(myDataSource);
+			return jdbcTemplate;
+		}
+
+		@Nonnull
+		public TransactionTemplate getTxTemplate() {
+			return myTxTemplate;
+		}
+
+		public void close() {
+			myDataSource.destroy();
+		}
+	}
+}

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

@@ -0,0 +1,165 @@
+package ca.uhn.fhir.jpa.migrate;
+
+import ca.uhn.fhir.jpa.migrate.taskdef.BaseTableColumnTypeTask;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.jdbc.core.ColumnMapRowMapper;
+import org.thymeleaf.util.StringUtils;
+
+import javax.sql.DataSource;
+import java.sql.*;
+import java.util.HashSet;
+import java.util.Locale;
+import java.util.Objects;
+import java.util.Set;
+
+public class JdbcUtils {
+	private static final Logger ourLog = LoggerFactory.getLogger(JdbcUtils.class);
+
+	/**
+	 * Retrieve all index names
+	 */
+	public static Set<String> getIndexNames(DriverTypeEnum.ConnectionProperties theConnectionProperties, String theTableName) throws SQLException {
+		DataSource dataSource = Objects.requireNonNull(theConnectionProperties.getDataSource());
+		Connection connection = dataSource.getConnection();
+		return theConnectionProperties.getTxTemplate().execute(t -> {
+			DatabaseMetaData metadata;
+			try {
+				metadata = connection.getMetaData();
+				ResultSet indexes = metadata.getIndexInfo(null, null, theTableName, false, false);
+
+				Set<String> indexNames = new HashSet<>();
+				while (indexes.next()) {
+
+					ourLog.debug("*** Next index: {}", new ColumnMapRowMapper().mapRow(indexes, 0));
+
+					String indexName = indexes.getString("INDEX_NAME");
+					indexName = StringUtils.toUpperCase(indexName, Locale.US);
+					indexNames.add(indexName);
+				}
+
+				return indexNames;
+			} catch (SQLException e) {
+				throw new InternalErrorException(e);
+			}
+		});
+
+	}
+
+	@SuppressWarnings("ConstantConditions")
+	public static boolean isIndexUnique(DriverTypeEnum.ConnectionProperties theConnectionProperties, String theTableName, String theIndexName) throws SQLException {
+		DataSource dataSource = Objects.requireNonNull(theConnectionProperties.getDataSource());
+		Connection connection = dataSource.getConnection();
+		return theConnectionProperties.getTxTemplate().execute(t -> {
+			DatabaseMetaData metadata;
+			try {
+				metadata = connection.getMetaData();
+				ResultSet indexes = metadata.getIndexInfo(null, null, theTableName, false, false);
+
+				while (indexes.next()) {
+					String indexName = indexes.getString("INDEX_NAME");
+					if (indexName.equalsIgnoreCase(theIndexName)) {
+						boolean nonUnique = indexes.getBoolean("NON_UNIQUE");
+						return !nonUnique;
+					}
+				}
+
+			} catch (SQLException e) {
+				throw new InternalErrorException(e);
+			}
+
+			throw new InternalErrorException("Can't find index: " + theIndexName + " on table " + theTableName);
+		});
+
+	}
+
+	/**
+	 * Retrieve all index names
+	 */
+	public static String getColumnType(DriverTypeEnum.ConnectionProperties theConnectionProperties, String theTableName, String theColumnName) throws SQLException {
+		DataSource dataSource = Objects.requireNonNull(theConnectionProperties.getDataSource());
+		try (Connection connection = dataSource.getConnection()) {
+			return theConnectionProperties.getTxTemplate().execute(t -> {
+				DatabaseMetaData metadata;
+				try {
+					metadata = connection.getMetaData();
+					ResultSet indexes = metadata.getColumns(null, null, theTableName, theColumnName);
+
+					indexes.next();
+
+					int dataType = indexes.getInt("DATA_TYPE");
+					Long length = indexes.getLong("COLUMN_SIZE");
+					switch (dataType) {
+						case Types.VARCHAR:
+							return BaseTableColumnTypeTask.ColumnTypeEnum.STRING.getDescriptor(length);
+						case Types.BIGINT:
+							return BaseTableColumnTypeTask.ColumnTypeEnum.LONG.getDescriptor(length);
+						default:
+							throw new IllegalArgumentException("Don't know how to handle datatype: " + dataType);
+					}
+
+				} catch (SQLException e) {
+					throw new InternalErrorException(e);
+				}
+
+			});
+		}
+	}
+
+	/**
+	 * Retrieve all index names
+	 */
+	public static Set<String> getColumnNames(DriverTypeEnum.ConnectionProperties theConnectionProperties, String theTableName) throws SQLException {
+		DataSource dataSource = Objects.requireNonNull(theConnectionProperties.getDataSource());
+		Connection connection = dataSource.getConnection();
+		return theConnectionProperties.getTxTemplate().execute(t -> {
+			DatabaseMetaData metadata;
+			try {
+				metadata = connection.getMetaData();
+				ResultSet indexes = metadata.getColumns(null, null, theTableName, null);
+
+				Set<String> columnNames = new HashSet<>();
+				while (indexes.next()) {
+					String columnName = indexes.getString("COLUMN_NAME");
+					columnName = StringUtils.toUpperCase(columnName, Locale.US);
+					columnNames.add(columnName);
+				}
+
+				return columnNames;
+			} catch (SQLException e) {
+				throw new InternalErrorException(e);
+			}
+		});
+
+	}
+
+	public static Set<String> getTableNames(DriverTypeEnum.ConnectionProperties theConnectionProperties) throws SQLException {
+		DataSource dataSource = Objects.requireNonNull(theConnectionProperties.getDataSource());
+		Connection connection = dataSource.getConnection();
+		return theConnectionProperties.getTxTemplate().execute(t -> {
+			DatabaseMetaData metadata;
+			try {
+				metadata = connection.getMetaData();
+				ResultSet tables = metadata.getTables(null, null, null, null);
+
+				Set<String> columnNames = new HashSet<>();
+				while (tables.next()) {
+					String tableName = tables.getString("TABLE_NAME");
+					tableName = StringUtils.toUpperCase(tableName, Locale.US);
+
+					String tableType = tables.getString("TABLE_TYPE");
+					if ("SYSTEM TABLE".equalsIgnoreCase(tableType)) {
+						continue;
+					}
+
+					columnNames.add(tableName);
+				}
+
+				return columnNames;
+			} catch (SQLException e) {
+				throw new InternalErrorException(e);
+			}
+		});
+	}
+}

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

@@ -0,0 +1,75 @@
+package ca.uhn.fhir.jpa.migrate;
+
+import ca.uhn.fhir.jpa.migrate.taskdef.BaseTask;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.List;
+
+public class Migrator {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(Migrator.class);
+	private DriverTypeEnum myDriverType;
+	private String myConnectionUrl;
+	private String myUsername;
+	private String myPassword;
+	private List<BaseTask> myTasks = new ArrayList<>();
+	private DriverTypeEnum.ConnectionProperties myConnectionProperties;
+	private int myChangesCount;
+	private boolean myDryRun;
+
+	public int getChangesCount() {
+		return myChangesCount;
+	}
+
+	public void setDriverType(DriverTypeEnum theDriverType) {
+		myDriverType = theDriverType;
+	}
+
+	public void setConnectionUrl(String theConnectionUrl) {
+		myConnectionUrl = theConnectionUrl;
+	}
+
+	public void setUsername(String theUsername) {
+		myUsername = theUsername;
+	}
+
+	public void setPassword(String thePassword) {
+		myPassword = thePassword;
+	}
+
+	public void addTask(BaseTask theTask) {
+		myTasks.add(theTask);
+	}
+
+	public void setDryRun(boolean theDryRun) {
+		myDryRun = theDryRun;
+	}
+
+	public void migrate() {
+		ourLog.info("Starting migration with {} tasks", myTasks.size());
+
+		myConnectionProperties = DriverTypeEnum.DERBY_EMBEDDED.newConnectionProperties(myConnectionUrl, myUsername, myPassword);
+		try {
+			for (BaseTask next : myTasks) {
+				next.setDriverType(myDriverType);
+				next.setConnectionProperties(myConnectionProperties);
+				next.setDryRun(myDryRun);
+				try {
+					next.execute();
+				} catch (SQLException e) {
+					throw new InternalErrorException("Failure executing task \"" + next.getDescription() + "\", aborting! Cause: " + e.toString(), e);
+				}
+
+				myChangesCount += next.getChangesCount();
+			}
+		} finally {
+			myConnectionProperties.close();
+		}
+
+		ourLog.info("Finished migration of {} tasks", myTasks.size());
+	}
+}

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

@@ -0,0 +1,30 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.jpa.migrate.JdbcUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.SQLException;
+import java.util.Set;
+
+public class AddColumnTask extends BaseTableColumnTypeTask<AddColumnTask> {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(AddColumnTask.class);
+
+
+	@Override
+	public void execute() throws SQLException {
+		Set<String> columnNames = JdbcUtils.getColumnNames(getConnectionProperties(), getTableName());
+		if (columnNames.contains(getColumnName())) {
+			ourLog.info("Column {} already exists on table {} - No action performed", getColumnName(), getTableName());
+			return;
+		}
+
+		String type = getSqlType();
+		String nullable = getSqlNotNull();
+		String sql = "alter table " + getTableName() + " add column " + getColumnName() + " " + type + " " + nullable;
+		ourLog.info("Adding column {} of type {} to table {}", getColumnName(), type, getTableName());
+		executeSql(sql);
+	}
+
+}

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

@@ -0,0 +1,59 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.jpa.migrate.JdbcUtils;
+import org.apache.commons.lang3.Validate;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.thymeleaf.util.StringUtils;
+
+import java.sql.SQLException;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Locale;
+import java.util.Set;
+
+public class AddIndexTask extends BaseTableTask<AddIndexTask> {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(AddIndexTask.class);
+	private String myIndexName;
+	private List<String> myColumns;
+	private Boolean myUnique;
+
+	public void setIndexName(String theIndexName) {
+		myIndexName = StringUtils.toUpperCase(theIndexName, Locale.US);
+	}
+
+	public void setColumns(List<String> theColumns) {
+		myColumns = theColumns;
+	}
+
+	public void setUnique(boolean theUnique) {
+		myUnique = theUnique;
+	}
+
+	@Override
+	public void validate() {
+		super.validate();
+		Validate.notBlank(myIndexName, "Index name not specified");
+		Validate.isTrue(myColumns.size() > 0, "Columns not specified");
+		Validate.notNull(myUnique, "Uniqueness not specified");
+	}
+
+	@Override
+	public void execute() throws SQLException {
+		Set<String> indexNames = JdbcUtils.getIndexNames(getConnectionProperties(), getTableName());
+		if (indexNames.contains(myIndexName)) {
+			ourLog.info("Index {} already exists on table {} - No action performed", myIndexName, getTableName());
+			return;
+		}
+
+		String unique = myUnique ? "UNIQUE " : "";
+		String columns = String.join(", ", myColumns);
+		String sql = "CREATE " + unique + " INDEX " + myIndexName + " ON " + getTableName() + "(" + columns + ")";
+		executeSql(sql);
+	}
+
+	public void setColumns(String... theColumns) {
+		setColumns(Arrays.asList(theColumns));
+	}
+}

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

@@ -0,0 +1,48 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
+import ca.uhn.fhir.jpa.migrate.JdbcUtils;
+import org.apache.commons.lang3.Validate;
+import org.intellij.lang.annotations.Language;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.jdbc.core.JdbcTemplate;
+
+import java.sql.SQLException;
+import java.util.*;
+
+public class AddTableTask extends BaseTableTask<AddTableTask> {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(AddTableTask.class);
+	private Map<DriverTypeEnum, List<String>> myDriverToSqls = new HashMap<>();
+
+	public void addSql(DriverTypeEnum theDriverType, @Language("SQL") String theSql) {
+		Validate.notNull(theDriverType);
+		Validate.notBlank(theSql);
+
+		List<String> list = myDriverToSqls.computeIfAbsent(theDriverType, t -> new ArrayList<>());
+		list.add(theSql);
+	}
+
+	@Override
+	public void execute() throws SQLException {
+		Set<String> tableNames = JdbcUtils.getTableNames(getConnectionProperties());
+		if (tableNames.contains(getTableName())) {
+			ourLog.info("Table {} already exists - No action performed", getTableName());
+			return;
+		}
+
+		List<String> sqlStatements = myDriverToSqls.get(getDriverType());
+		ourLog.info("Going to create table {} using {} SQL statements", getTableName(), sqlStatements.size());
+		getConnectionProperties().getTxTemplate().execute(t->{
+
+			JdbcTemplate jdbcTemplate = getConnectionProperties().newJdbcTemplate();
+			for (String nextSql : sqlStatements) {
+				jdbcTemplate.execute(nextSql);
+			}
+
+			return null;
+		});
+
+	}
+}

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

@@ -0,0 +1,95 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.jdbc.core.ColumnMapRowMapper;
+import org.springframework.jdbc.core.JdbcTemplate;
+
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.function.Consumer;
+
+public class ArbitrarySqlTask extends BaseTask<ArbitrarySqlTask> {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(ArbitrarySqlTask.class);
+	private final String myDescription;
+	private List<Task> myTask = new ArrayList<>();
+	private int myBatchSize = 1000;
+
+	public ArbitrarySqlTask(String theDescription) {
+		myDescription = theDescription;
+	}
+
+	public void addQuery(String theSql, QueryModeEnum theMode, Consumer<Map<String, Object>> theConsumer) {
+		myTask.add(new QueryTask(theSql, theMode, theConsumer));
+	}
+
+	@Override
+	public void validate() {
+		// nothing
+	}
+
+	@Override
+	public void execute() throws SQLException {
+		ourLog.info("Starting: {}", myDescription);
+
+		for (Task next : myTask) {
+			next.execute();
+		}
+
+	}
+
+	public void setBatchSize(int theBatchSize) {
+		myBatchSize = theBatchSize;
+	}
+
+	public enum QueryModeEnum {
+		BATCH_UNTIL_NO_MORE
+	}
+
+	private abstract class Task {
+		public abstract void execute();
+	}
+
+	private class QueryTask extends Task {
+		private final String mySql;
+		private final QueryModeEnum myMode;
+		private final Consumer<Map<String, Object>> myConsumer;
+
+		public QueryTask(String theSql, QueryModeEnum theMode, Consumer<Map<String, Object>> theConsumer) {
+			mySql = theSql;
+			myMode = theMode;
+			myConsumer = theConsumer;
+		}
+
+
+		@Override
+		public void execute() {
+			if (isDryRun()) {
+				logDryRunSql(mySql);
+				return;
+			}
+
+			List<Map<String, Object>> rows;
+			do {
+				ourLog.info("Querying for up to {} rows", myBatchSize);
+				rows = getTxTemplate().execute(t -> {
+					JdbcTemplate jdbcTemplate = newJdbcTemnplate();
+					jdbcTemplate.setMaxRows(myBatchSize);
+					return jdbcTemplate.query(mySql, new ColumnMapRowMapper());
+				});
+
+				ourLog.info("Processing {} rows", rows.size());
+				List<Map<String, Object>> finalRows = rows;
+				getTxTemplate().execute(t -> {
+					for (Map<String, Object> nextRow : finalRows) {
+						myConsumer.accept(nextRow);
+					}
+					return null;
+				});
+			} while (rows.size() > 0);
+		}
+	}
+}

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

@@ -0,0 +1,30 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import org.apache.commons.lang3.Validate;
+import org.thymeleaf.util.StringUtils;
+
+import java.util.Locale;
+
+public abstract class BaseTableColumnTask<T extends BaseTableTask> extends BaseTableTask<T> {
+
+	private String myColumnName;
+
+	@SuppressWarnings("unchecked")
+	public T setColumnName(String theColumnName) {
+		myColumnName = StringUtils.toUpperCase(theColumnName, Locale.US);
+		return (T) this;
+	}
+
+
+	public String getColumnName() {
+		return myColumnName;
+	}
+
+	@Override
+	public void validate() {
+		super.validate();
+		Validate.notBlank(myColumnName, "Column name not specified");
+	}
+
+
+}

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

@@ -0,0 +1,136 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
+import org.apache.commons.lang3.Validate;
+import org.springframework.util.Assert;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Objects;
+
+public abstract class BaseTableColumnTypeTask<T extends BaseTableTask> extends BaseTableColumnTask<T> {
+
+	private ColumnTypeEnum myColumnType;
+	private Map<ColumnTypeEnum, Map<DriverTypeEnum, String>> myColumnTypeToDriverTypeToSqlType = new HashMap<>();
+	private Boolean myNullable;
+	private Long myColumnLength;
+
+	/**
+	 * Constructor
+	 */
+	BaseTableColumnTypeTask() {
+		setColumnType(ColumnTypeEnum.LONG, DriverTypeEnum.DERBY_EMBEDDED, "bigint");
+		setColumnType(ColumnTypeEnum.LONG, DriverTypeEnum.MARIADB_10_1, "bigint");
+		setColumnType(ColumnTypeEnum.LONG, DriverTypeEnum.MYSQL_5_7, "bigint");
+		setColumnType(ColumnTypeEnum.LONG, DriverTypeEnum.MSSQL_2012, "bigint");
+		setColumnType(ColumnTypeEnum.LONG, DriverTypeEnum.ORACLE_12C, "number(19,0)");
+		setColumnType(ColumnTypeEnum.LONG, DriverTypeEnum.POSTGRES_9_4, "int8");
+
+		setColumnType(ColumnTypeEnum.STRING, DriverTypeEnum.DERBY_EMBEDDED, "varchar(?)");
+		setColumnType(ColumnTypeEnum.STRING, DriverTypeEnum.MARIADB_10_1, "varchar(?)");
+		setColumnType(ColumnTypeEnum.STRING, DriverTypeEnum.MYSQL_5_7, "varchar(?)");
+		setColumnType(ColumnTypeEnum.STRING, DriverTypeEnum.MSSQL_2012, "varchar(?)");
+		setColumnType(ColumnTypeEnum.STRING, DriverTypeEnum.ORACLE_12C, "varchar2(?)");
+		setColumnType(ColumnTypeEnum.STRING, DriverTypeEnum.POSTGRES_9_4, "varchar(?)");
+
+		setColumnType(ColumnTypeEnum.DATE_TIMESTAMPT, DriverTypeEnum.DERBY_EMBEDDED, "timestamp");
+		setColumnType(ColumnTypeEnum.DATE_TIMESTAMPT, DriverTypeEnum.MARIADB_10_1, "datetime(6)");
+		setColumnType(ColumnTypeEnum.DATE_TIMESTAMPT, DriverTypeEnum.MYSQL_5_7, "datetime(6)");
+		setColumnType(ColumnTypeEnum.DATE_TIMESTAMPT, DriverTypeEnum.MSSQL_2012, "datetime2");
+		setColumnType(ColumnTypeEnum.DATE_TIMESTAMPT, DriverTypeEnum.ORACLE_12C, "timestamp");
+		setColumnType(ColumnTypeEnum.DATE_TIMESTAMPT, DriverTypeEnum.POSTGRES_9_4, "timestamp");
+	}
+
+	public ColumnTypeEnum getColumnType() {
+		return myColumnType;
+	}
+
+	private void setColumnType(ColumnTypeEnum theColumnType, DriverTypeEnum theDriverType, String theColumnTypeSql) {
+		Map<DriverTypeEnum, String> columnSqlType = myColumnTypeToDriverTypeToSqlType.computeIfAbsent(theColumnType, k -> new HashMap<>());
+		if (columnSqlType.containsKey(theDriverType)) {
+			throw new IllegalStateException("Duplicate key: " + theDriverType);
+		}
+		columnSqlType.put(theDriverType, theColumnTypeSql);
+	}
+
+
+	@Override
+	public void validate() {
+		super.validate();
+		Validate.notNull(myColumnType);
+		Validate.notNull(myNullable);
+
+		if (myColumnType == ColumnTypeEnum.STRING) {
+			Validate.notNull(myColumnLength);
+		} else {
+			Validate.isTrue(myColumnLength == null);
+		}
+	}
+
+	@SuppressWarnings("unchecked")
+	public T setColumnType(ColumnTypeEnum theColumnType) {
+		myColumnType = theColumnType;
+		return (T) this;
+	}
+
+	protected String getSqlType() {
+		String retVal = myColumnTypeToDriverTypeToSqlType.get(myColumnType).get(getDriverType());
+		Objects.requireNonNull(retVal);
+
+		if (myColumnType == ColumnTypeEnum.STRING) {
+			retVal = retVal.replace("?", Long.toString(getColumnLength()));
+		}
+
+		return retVal;
+	}
+
+	public boolean isNullable() {
+		return myNullable;
+	}
+
+	public void setNullable(boolean theNullable) {
+		myNullable = theNullable;
+	}
+
+	protected String getSqlNotNull() {
+		return isNullable() ? "" : " not null";
+	}
+
+	public Long getColumnLength() {
+		return myColumnLength;
+	}
+
+	public void setColumnLength(int theColumnLength) {
+		myColumnLength = (long) theColumnLength;
+	}
+
+
+	public enum ColumnTypeEnum {
+
+		LONG {
+			@Override
+			public String getDescriptor(Long theColumnLength) {
+				Assert.isTrue(theColumnLength == null, "Must not supply a column length");
+				return "bigint";
+			}
+		},
+		STRING {
+			@Override
+			public String getDescriptor(Long theColumnLength) {
+				Assert.isTrue(theColumnLength != null, "Must supply a column length");
+				return "varchar(" + theColumnLength + ")";
+			}
+		},
+		DATE_TIMESTAMPT{
+			@Override
+			public String getDescriptor(Long theColumnLength) {
+				Assert.isTrue(theColumnLength == null, "Must not supply a column length");
+				return "timestamp";
+			}
+		};
+
+		public abstract String getDescriptor(Long theColumnLength);
+
+	}
+
+}

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

@@ -0,0 +1,21 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import org.apache.commons.lang3.Validate;
+
+public abstract class BaseTableTask<T extends BaseTableTask> extends BaseTask {
+	private String myTableName;
+
+	public String getTableName() {
+		return myTableName;
+	}
+
+	public T setTableName(String theTableName) {
+		myTableName = theTableName;
+		return (T) this;
+	}
+
+	@Override
+	public void validate() {
+		Validate.notBlank(myTableName);
+	}
+}

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

@@ -0,0 +1,91 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
+import org.intellij.lang.annotations.Language;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.jdbc.core.JdbcTemplate;
+import org.springframework.transaction.support.TransactionTemplate;
+
+import java.sql.SQLException;
+
+public abstract class BaseTask<T extends BaseTask> {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(BaseTask.class);
+	private DriverTypeEnum.ConnectionProperties myConnectionProperties;
+	private DriverTypeEnum myDriverType;
+	private String myDescription;
+	private int myChangesCount;
+	private boolean myDryRun;
+
+	public boolean isDryRun() {
+		return myDryRun;
+	}
+
+	public void setDryRun(boolean theDryRun) {
+		myDryRun = theDryRun;
+	}
+
+	public String getDescription() {
+		return myDescription;
+	}
+
+	@SuppressWarnings("unchecked")
+	public T setDescription(String theDescription) {
+		myDescription = theDescription;
+		return (T) this;
+	}
+
+	public int getChangesCount() {
+		return myChangesCount;
+	}
+
+	public void executeSql(@Language("SQL") String theSql, Object... theArguments) {
+		if (isDryRun()) {
+			logDryRunSql(theSql);
+			return;
+		}
+
+		Integer changes = getConnectionProperties().getTxTemplate().execute(t -> {
+			JdbcTemplate jdbcTemplate = getConnectionProperties().newJdbcTemplate();
+			int changesCount = jdbcTemplate.update(theSql, theArguments);
+			ourLog.info("SQL \"{}\" returned {}", theSql, changesCount);
+			return changesCount;
+		});
+
+		myChangesCount += changes;
+
+	}
+
+	protected void logDryRunSql(@Language("SQL") String theSql) {
+		ourLog.info("WOULD EXECUTE SQL: {}", theSql);
+	}
+
+	public DriverTypeEnum.ConnectionProperties getConnectionProperties() {
+		return myConnectionProperties;
+	}
+
+	public void setConnectionProperties(DriverTypeEnum.ConnectionProperties theConnectionProperties) {
+		myConnectionProperties = theConnectionProperties;
+	}
+
+	public DriverTypeEnum getDriverType() {
+		return myDriverType;
+	}
+
+	public void setDriverType(DriverTypeEnum theDriverType) {
+		myDriverType = theDriverType;
+	}
+
+	public abstract void validate();
+
+	public TransactionTemplate getTxTemplate() {
+		return getConnectionProperties().getTxTemplate();
+	}
+
+	public JdbcTemplate newJdbcTemnplate() {
+		return getConnectionProperties().newJdbcTemplate();
+	}
+
+	public abstract void execute() throws SQLException;
+}

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

@@ -0,0 +1,133 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.util.StopWatch;
+import com.google.common.collect.ForwardingMap;
+import org.apache.commons.lang3.Validate;
+import org.checkerframework.checker.nullness.compatqual.NullableDecl;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.jdbc.core.JdbcTemplate;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.function.Function;
+
+public class CalculateHashesTask extends BaseTableColumnTask<CalculateHashesTask> {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(CalculateHashesTask.class);
+	private int myBatchSize = 10000;
+	private Map<String, Function<MandatoryKeyMap<String, Object>, Long>> myCalculators = new HashMap<>();
+
+	public void setBatchSize(int theBatchSize) {
+		myBatchSize = theBatchSize;
+	}
+
+
+	@Override
+	public void execute() {
+		if (isDryRun()) {
+			return;
+		}
+
+		List<Map<String, Object>> rows;
+		do {
+			rows = getTxTemplate().execute(t -> {
+				JdbcTemplate jdbcTemplate = newJdbcTemnplate();
+				jdbcTemplate.setMaxRows(myBatchSize);
+				String sql = "SELECT * FROM " + getTableName() + " WHERE " + getColumnName() + " IS NULL";
+				ourLog.info("Finding up to {} rows in {} that requires hashes", myBatchSize, getTableName());
+				return jdbcTemplate.queryForList(sql);
+			});
+
+			updateRows(rows);
+		} while (rows.size() > 0);
+	}
+
+	private void updateRows(List<Map<String, Object>> theRows) {
+		StopWatch sw = new StopWatch();
+		getTxTemplate().execute(t -> {
+
+			// Loop through rows
+			assert theRows != null;
+			for (Map<String, Object> nextRow : theRows) {
+
+				Map<String, Long> newValues = new HashMap<>();
+				MandatoryKeyMap<String, Object> nextRowMandatoryKeyMap = new MandatoryKeyMap<>(nextRow);
+
+				// Apply calculators
+				for (Map.Entry<String, Function<MandatoryKeyMap<String, Object>, Long>> nextCalculatorEntry : myCalculators.entrySet()) {
+					String nextColumn = nextCalculatorEntry.getKey();
+					Function<MandatoryKeyMap<String, Object>, Long> nextCalculator = nextCalculatorEntry.getValue();
+					Long value = nextCalculator.apply(nextRowMandatoryKeyMap);
+					newValues.put(nextColumn, value);
+				}
+
+				// Generate update SQL
+				StringBuilder sqlBuilder = new StringBuilder();
+				List<Long> arguments = new ArrayList<>();
+				sqlBuilder.append("UPDATE ");
+				sqlBuilder.append(getTableName());
+				sqlBuilder.append(" SET ");
+				for (Map.Entry<String, Long> nextNewValueEntry : newValues.entrySet()) {
+					if (arguments.size() > 0) {
+						sqlBuilder.append(", ");
+					}
+					sqlBuilder.append(nextNewValueEntry.getKey()).append(" = ?");
+					arguments.add(nextNewValueEntry.getValue());
+				}
+				sqlBuilder.append(" WHERE SP_ID = ?");
+				arguments.add((Long) nextRow.get("SP_ID"));
+
+				// Apply update SQL
+				newJdbcTemnplate().update(sqlBuilder.toString(), arguments.toArray());
+
+			}
+
+			return theRows.size();
+		});
+		ourLog.info("Updated {} rows on {} in {}", theRows.size(), getTableName(), sw.toString());
+	}
+
+	public CalculateHashesTask addCalculator(String theColumnName, Function<MandatoryKeyMap<String, Object>, Long> theConsumer) {
+		Validate.isTrue(myCalculators.containsKey(theColumnName) == false);
+		myCalculators.put(theColumnName, theConsumer);
+		return this;
+	}
+
+
+	public static class MandatoryKeyMap<K, V> extends ForwardingMap<K, V> {
+
+		private final Map<K, V> myWrap;
+
+		public MandatoryKeyMap(Map<K, V> theWrap) {
+			myWrap = theWrap;
+		}
+
+		@Override
+		public V get(@NullableDecl Object theKey) {
+			if (!containsKey(theKey)) {
+				throw new IllegalArgumentException("No key: " + theKey);
+			}
+			return super.get(theKey);
+		}
+
+		public String getString(String theKey) {
+			return (String) get(theKey);
+		}
+
+		@Override
+		protected Map<K, V> delegate() {
+			return myWrap;
+		}
+
+		public String getResourceType() {
+			return getString("RES_TYPE");
+		}
+
+		public String getParamName() {
+			return getString("SP_NAME");
+		}
+	}
+}

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

@@ -0,0 +1,83 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.jpa.migrate.JdbcUtils;
+import org.apache.commons.lang3.Validate;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.SQLException;
+import java.util.Set;
+
+public class DropIndexTask extends BaseTableTask<DropIndexTask> {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(DropIndexTask.class);
+	private String myIndexName;
+
+	@Override
+	public void validate() {
+		super.validate();
+		Validate.notBlank(myIndexName, "The index name must not be blank");
+
+		if (getDescription() == null) {
+			setDescription("Drop index " + myIndexName + " on table " + getTableName());
+		}
+	}
+
+	@Override
+	public void execute() throws SQLException {
+		Set<String> indexNames = JdbcUtils.getIndexNames(getConnectionProperties(), getTableName());
+
+		if (!indexNames.contains(myIndexName)) {
+			ourLog.info("Index {} does not exist on table {} - No action needed", myIndexName, getTableName());
+			return;
+		}
+
+		boolean isUnique = JdbcUtils.isIndexUnique(getConnectionProperties(), getTableName(), myIndexName);
+		String uniquenessString = isUnique ? "unique" : "non-unique";
+		ourLog.info("Dropping {} index {} on table {}", uniquenessString, myIndexName, getTableName());
+
+		String sql = null;
+
+		if (isUnique) {
+			// Drop constraint
+			switch (getDriverType()) {
+				case MYSQL_5_7:
+				case MARIADB_10_1:
+					sql = "ALTER TABLE " + getTableName() + " DROP INDEX " + myIndexName;
+					break;
+				case DERBY_EMBEDDED:
+					sql = "DROP INDEX " + myIndexName;
+					break;
+				case POSTGRES_9_4:
+				case ORACLE_12C:
+				case MSSQL_2012:
+					sql = "ALTER TABLE " + getTableName() + " DROP CONSTRAINT " + myIndexName;
+					break;
+			}
+		} else {
+			// Drop index
+			switch (getDriverType()) {
+				case MYSQL_5_7:
+				case MARIADB_10_1:
+					sql = "ALTER TABLE " + getTableName() + " DROP INDEX " + myIndexName;
+					break;
+				case POSTGRES_9_4:
+				case DERBY_EMBEDDED:
+				case ORACLE_12C:
+					sql = "DROP INDEX " + myIndexName;
+					break;
+				case MSSQL_2012:
+					sql = "DROP INDEX " + getTableName() + "." + myIndexName;
+					break;
+			}
+		}
+		executeSql(sql);
+
+	}
+
+
+	public DropIndexTask setIndexName(String theIndexName) {
+		myIndexName = theIndexName;
+		return this;
+	}
+}

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

@@ -0,0 +1,27 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import org.apache.commons.lang3.StringUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class LogStartSectionWithMessageTask extends BaseTask {
+	private static final Logger ourLog = LoggerFactory.getLogger(LogStartSectionWithMessageTask.class);
+	private final String myMessage;
+
+	public LogStartSectionWithMessageTask(String theMessage) {
+		myMessage = theMessage;
+	}
+
+	@Override
+	public void validate() {
+		// nothing
+	}
+
+	@Override
+	public void execute() {
+		ourLog.info("");
+		ourLog.info(StringUtils.leftPad("", myMessage.length(), "*"));
+		ourLog.info(myMessage);
+		ourLog.info(StringUtils.leftPad("", myMessage.length(), "*"));
+	}
+}

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

@@ -0,0 +1,69 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.jpa.migrate.JdbcUtils;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.SQLException;
+
+public class ModifyColumnTask extends BaseTableColumnTypeTask<ModifyColumnTask> {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(ModifyColumnTask.class);
+
+
+	@Override
+	public void execute() {
+
+		String existingType;
+		try {
+			existingType = JdbcUtils.getColumnType(getConnectionProperties(), getTableName(), getColumnName());
+		} catch (SQLException e) {
+			throw new InternalErrorException(e);
+		}
+
+		String wantedType = getColumnType().getDescriptor(getColumnLength());
+		if (existingType.equals(wantedType)) {
+			ourLog.info("Column {} on table {} is already of type {} - No action performed", getColumnName(), getTableName(), wantedType);
+			return;
+		}
+
+		String type = getSqlType();
+		String notNull = getSqlNotNull();
+
+		String sql;
+		String sqlNotNull = null;
+		switch (getDriverType()) {
+			case DERBY_EMBEDDED:
+				sql = "alter table " + getTableName() + " alter column " + getColumnName() + " set data type " + type;
+				break;
+			case MARIADB_10_1:
+			case MYSQL_5_7:
+				sql = "alter table " + getTableName() + " modify column " + getColumnName() + " " + type + notNull;
+				break;
+			case POSTGRES_9_4:
+				sql = "alter table " + getTableName() + " alter column " + getColumnName() + " type " + type;
+				if (isNullable() == false) {
+					sqlNotNull = "alter table " + getTableName() + " alter column " + getColumnName() + " set not null";
+				}
+				break;
+			case ORACLE_12C:
+				sql = "alter table " + getTableName() + " modify " + getColumnName() + " " + type + notNull;
+				break;
+			case MSSQL_2012:
+				sql = "alter table " + getTableName() + " alter column " + getColumnName() + " " + type + notNull;
+				break;
+			default:
+				throw new IllegalStateException("Dont know how to handle " + getDriverType());
+		}
+
+		ourLog.info("Updating column {} on table {} to type {}", getColumnName(), getTableName(), type);
+		executeSql(sql);
+
+		if (sqlNotNull != null) {
+			ourLog.info("Updating column {} on table {} to not null", getColumnName(), getTableName());
+			executeSql(sqlNotNull);
+		}
+	}
+
+}

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

@@ -0,0 +1,406 @@
+package ca.uhn.fhir.jpa.migrate.tasks;
+
+import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.entity.*;
+import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
+import ca.uhn.fhir.jpa.migrate.taskdef.AddColumnTask;
+import ca.uhn.fhir.jpa.migrate.taskdef.ArbitrarySqlTask;
+import ca.uhn.fhir.jpa.migrate.taskdef.BaseTableColumnTypeTask;
+import ca.uhn.fhir.jpa.migrate.taskdef.CalculateHashesTask;
+import ca.uhn.fhir.jpa.migrate.tasks.api.BaseMigrationTasks;
+import ca.uhn.fhir.util.VersionEnum;
+
+@SuppressWarnings({"UnstableApiUsage", "SqlNoDataSourceInspection", "SpellCheckingInspection"})
+public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks {
+
+	/**
+	 * Constructor
+	 */
+	public HapiFhirJpaMigrationTasks() {
+		init350();
+	}
+
+	private void init350() {
+		Builder version = forVersion(VersionEnum.V3_5_0);
+
+		// Forced ID changes
+		Builder.BuilderWithTableName forcedId = version.onTable("HFJ_FORCED_ID");
+		version.startSectionWithMessage("Starting work on table: " + forcedId.getTableName());
+		forcedId
+			.dropIndex("IDX_FORCEDID_TYPE_FORCEDID");
+		forcedId
+			.dropIndex("IDX_FORCEDID_TYPE_RESID");
+		forcedId
+			.addIndex("IDX_FORCEDID_TYPE_FID")
+			.unique(true)
+			.withColumns("RESOURCE_TYPE", "FORCED_ID");
+
+		// Indexes - Coords
+		Builder.BuilderWithTableName spidxCoords = version.onTable("HFJ_SPIDX_COORDS");
+		version.startSectionWithMessage("Starting work on table: " + spidxCoords.getTableName());
+		spidxCoords
+			.dropIndex("IDX_SP_COORDS");
+		spidxCoords
+			.addColumn("HASH_IDENTITY")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxCoords
+			.addIndex("IDX_SP_COORDS_HASH")
+			.unique(false)
+			.withColumns("HASH_IDENTITY", "SP_LATITUDE", "SP_LONGITUDE");
+		spidxCoords
+			.addTask(new CalculateHashesTask()
+				.setColumnName("HASH_IDENTITY")
+				.addCalculator("HASH_IDENTITY", t -> BaseResourceIndexedSearchParam.calculateHashIdentity(t.getResourceType(), t.getString("SP_NAME")))
+			);
+
+		// Indexes - Date
+		Builder.BuilderWithTableName spidxDate = version.onTable("HFJ_SPIDX_DATE");
+		version.startSectionWithMessage("Starting work on table: " + spidxDate.getTableName());
+		spidxDate
+			.dropIndex("IDX_SP_TOKEN");
+		spidxDate
+			.addColumn("HASH_IDENTITY")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxDate
+			.addIndex("IDX_SP_DATE_HASH")
+			.unique(false)
+			.withColumns("HASH_IDENTITY", "SP_VALUE_LOW", "SP_VALUE_HIGH");
+		spidxDate
+			.addTask(new CalculateHashesTask()
+				.setColumnName("HASH_IDENTITY")
+				.addCalculator("HASH_IDENTITY", t -> BaseResourceIndexedSearchParam.calculateHashIdentity(t.getResourceType(), t.getString("SP_NAME")))
+			);
+
+		// Indexes - Number
+		Builder.BuilderWithTableName spidxNumber = version.onTable("HFJ_SPIDX_NUMBER");
+		version.startSectionWithMessage("Starting work on table: " + spidxNumber.getTableName());
+		spidxNumber
+			.dropIndex("IDX_SP_NUMBER");
+		spidxNumber
+			.addColumn("HASH_IDENTITY")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxNumber
+			.addIndex("IDX_SP_NUMBER_HASH_VAL")
+			.unique(false)
+			.withColumns("HASH_IDENTITY", "SP_VALUE");
+		spidxNumber
+			.addTask(new CalculateHashesTask()
+				.setColumnName("HASH_IDENTITY")
+				.addCalculator("HASH_IDENTITY", t -> BaseResourceIndexedSearchParam.calculateHashIdentity(t.getResourceType(), t.getString("SP_NAME")))
+			);
+
+		// Indexes - Quantity
+		Builder.BuilderWithTableName spidxQuantity = version.onTable("HFJ_SPIDX_QUANTITY");
+		version.startSectionWithMessage("Starting work on table: " + spidxQuantity.getTableName());
+		spidxQuantity
+			.dropIndex("IDX_SP_QUANTITY");
+		spidxQuantity
+			.addColumn("HASH_IDENTITY")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxQuantity
+			.addColumn("HASH_IDENTITY_SYS_UNITS")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxQuantity
+			.addColumn("HASH_IDENTITY_AND_UNITS")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxQuantity
+			.addIndex("IDX_SP_QUANTITY_HASH")
+			.unique(false)
+			.withColumns("HASH_IDENTITY", "SP_VALUE");
+		spidxQuantity
+			.addIndex("IDX_SP_QUANTITY_HASH_UN")
+			.unique(false)
+			.withColumns("HASH_IDENTITY_AND_UNITS", "SP_VALUE");
+		spidxQuantity
+			.addIndex("IDX_SP_QUANTITY_HASH_SYSUN")
+			.unique(false)
+			.withColumns("HASH_IDENTITY_SYS_UNITS", "SP_VALUE");
+		spidxQuantity
+			.addTask(new CalculateHashesTask()
+				.setColumnName("HASH_IDENTITY")
+				.addCalculator("HASH_IDENTITY", t -> BaseResourceIndexedSearchParam.calculateHashIdentity(t.getResourceType(), t.getString("SP_NAME")))
+				.addCalculator("HASH_IDENTITY_AND_UNITS", t -> ResourceIndexedSearchParamQuantity.calculateHashUnits(t.getResourceType(), t.getString("SP_NAME"), t.getString("SP_UNITS")))
+				.addCalculator("HASH_IDENTITY_SYS_UNITS", t -> ResourceIndexedSearchParamQuantity.calculateHashSystemAndUnits(t.getResourceType(), t.getString("SP_NAME"), t.getString("SP_SYSTEM"), t.getString("SP_UNITS")))
+			);
+
+		// Indexes - String
+		Builder.BuilderWithTableName spidxString = version.onTable("HFJ_SPIDX_STRING");
+		version.startSectionWithMessage("Starting work on table: " + spidxString.getTableName());
+		spidxString
+			.dropIndex("IDX_SP_STRING");
+		spidxString
+			.addColumn("HASH_NORM_PREFIX")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxString
+			.addIndex("IDX_SP_STRING_HASH_NRM")
+			.unique(false)
+			.withColumns("HASH_NORM_PREFIX", "SP_VALUE_NORMALIZED");
+		spidxString
+			.addIndex("IDX_SP_STRING_HASH_EXCT")
+			.unique(false)
+			.withColumns("HASH_EXACT");
+		spidxString
+			.addTask(new CalculateHashesTask()
+				.setColumnName("HASH_NORM_PREFIX")
+				.addCalculator("HASH_NORM_PREFIX", t -> ResourceIndexedSearchParamString.calculateHashNormalized(new DaoConfig(), t.getResourceType(), t.getString("SP_NAME"), t.getString("SP_VALUE_NORMALIZED")))
+				.addCalculator("HASH_EXACT", t -> ResourceIndexedSearchParamString.calculateHashExact(t.getResourceType(), t.getParamName(), t.getString("SP_VALUE_EXACT")))
+			);
+
+		// Indexes - Token
+		Builder.BuilderWithTableName spidxToken = version.onTable("HFJ_SPIDX_TOKEN");
+		version.startSectionWithMessage("Starting work on table: " + spidxToken.getTableName());
+		spidxToken
+			.dropIndex("IDX_SP_TOKEN");
+		spidxToken
+			.dropIndex("IDX_SP_TOKEN_UNQUAL");
+		spidxToken
+			.addColumn("HASH_IDENTITY")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxToken
+			.addColumn("HASH_SYS")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxToken
+			.addColumn("HASH_SYS_AND_VALUE")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxToken
+			.addColumn("HASH_VALUE")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxToken
+			.addIndex("IDX_SP_TOKEN_HASH")
+			.unique(false)
+			.withColumns("HASH_IDENTITY");
+		spidxToken
+			.addIndex("IDX_SP_TOKEN_HASH_S")
+			.unique(false)
+			.withColumns("HASH_SYS");
+		spidxToken
+			.addIndex("IDX_SP_TOKEN_HASH_SV")
+			.unique(false)
+			.withColumns("HASH_SYS_AND_VALUE");
+		spidxToken
+			.addIndex("IDX_SP_TOKEN_HASH_V")
+			.unique(false)
+			.withColumns("HASH_VALUE");
+		spidxToken
+			.addTask(new CalculateHashesTask()
+				.setColumnName("HASH_IDENTITY")
+				.addCalculator("HASH_IDENTITY", t -> BaseResourceIndexedSearchParam.calculateHashIdentity(t.getResourceType(), t.getString("SP_NAME")))
+				.addCalculator("HASH_SYS", t -> ResourceIndexedSearchParamToken.calculateHashSystem(t.getResourceType(), t.getParamName(), t.getString("SP_SYSTEM")))
+				.addCalculator("HASH_SYS_AND_VALUE", t -> ResourceIndexedSearchParamToken.calculateHashSystemAndValue(t.getResourceType(), t.getParamName(), t.getString("SP_SYSTEM"), t.getString("SP_VALUE")))
+				.addCalculator("HASH_VALUE", t -> ResourceIndexedSearchParamToken.calculateHashValue(t.getResourceType(), t.getParamName(), t.getString("SP_VALUE")))
+			);
+
+		// Indexes - URI
+		Builder.BuilderWithTableName spidxUri = version.onTable("HFJ_SPIDX_URI");
+		version.startSectionWithMessage("Starting work on table: " + spidxUri.getTableName());
+		spidxUri
+			.addColumn("HASH_IDENTITY")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxUri
+			.addIndex("IDX_SP_URI_HASH_IDENTITY")
+			.unique(false)
+			.withColumns("HASH_IDENTITY", "SP_URI");
+		spidxUri
+			.addIndex("IDX_SP_URI_HASH_URI")
+			.unique(false)
+			.withColumns("HASH_URI");
+		spidxUri
+			.addTask(new CalculateHashesTask()
+				.setColumnName("HASH_IDENTITY")
+				.addCalculator("HASH_IDENTITY", t -> BaseResourceIndexedSearchParam.calculateHashIdentity(t.getResourceType(), t.getString("SP_NAME")))
+				.addCalculator("HASH_URI", t -> ResourceIndexedSearchParamUri.calculateHashUri(t.getResourceType(), t.getString("SP_NAME"), t.getString("SP_URI")))
+			);
+
+		// Search Parameter Presence
+		Builder.BuilderWithTableName spp = version.onTable("HFJ_RES_PARAM_PRESENT");
+		version.startSectionWithMessage("Starting work on table: " + spp.getTableName());
+		spp.dropIndex("IDX_RESPARMPRESENT_SPID_RESID");
+		spp
+			.addColumn("HASH_PRESENCE")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spp
+			.addIndex("IDX_RESPARMPRESENT_HASHPRES")
+			.unique(false)
+			.withColumns("HASH_PRESENCE");
+		ArbitrarySqlTask consolidateSearchParamPresenceIndexesTask = new ArbitrarySqlTask("Consolidate search parameter presence indexes");
+		consolidateSearchParamPresenceIndexesTask.setBatchSize(1);
+		String sql = "SELECT " +
+			"HFJ_SEARCH_PARM.RES_TYPE RES_TYPE, HFJ_SEARCH_PARM.PARAM_NAME PARAM_NAME, " +
+			"HFJ_RES_PARAM_PRESENT.PID PID, HFJ_RES_PARAM_PRESENT.SP_ID SP_ID, HFJ_RES_PARAM_PRESENT.SP_PRESENT SP_PRESENT, HFJ_RES_PARAM_PRESENT.HASH_PRESENCE HASH_PRESENCE " +
+			"from HFJ_RES_PARAM_PRESENT " +
+			"join HFJ_SEARCH_PARM ON (HFJ_SEARCH_PARM.PID = HFJ_RES_PARAM_PRESENT.SP_ID) " +
+			"where HFJ_RES_PARAM_PRESENT.HASH_PRESENCE is null";
+		consolidateSearchParamPresenceIndexesTask.addQuery(sql, ArbitrarySqlTask.QueryModeEnum.BATCH_UNTIL_NO_MORE, t -> {
+			Long pid = (Long) t.get("PID");
+			Boolean present = (Boolean) t.get("HASH_PRESENCE");
+			String resType = (String) t.get("RES_TYPE");
+			String paramName = (String) t.get("PARAM_NAME");
+			Long hash = SearchParamPresent.calculateHashPresence(resType, paramName, present);
+			consolidateSearchParamPresenceIndexesTask.executeSql("update HFJ_RES_PARAM_PRESENT set HASH_PRESENCE = ? where PID = ?", hash, pid);
+		});
+		version.addTask(consolidateSearchParamPresenceIndexesTask);
+
+		// Concept
+		Builder.BuilderWithTableName trmConcept = version.onTable("TRM_CONCEPT");
+		version.startSectionWithMessage("Starting work on table: " + trmConcept.getTableName());
+		trmConcept
+			.addColumn("CONCEPT_UPDATED")
+			.nullable()
+			.type(BaseTableColumnTypeTask.ColumnTypeEnum.DATE_TIMESTAMPT);
+		trmConcept
+			.addIndex("IDX_CONCEPT_UPDATED")
+			.unique(false)
+			.withColumns("CONCEPT_UPDATED");
+		trmConcept
+			.modifyColumn("CODE")
+			.nonNullable()
+			.withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 500);
+
+		// Concept Designation
+		version.startSectionWithMessage("Starting work on table: TRM_CONCEPT_DESIG");
+		version
+			.addTable("TRM_CONCEPT_DESIG")
+			.addSql(DriverTypeEnum.DERBY_EMBEDDED, "create table TRM_CONCEPT_DESIG (PID bigint not null, LANG varchar(500), USE_CODE varchar(500), USE_DISPLAY varchar(500), USE_SYSTEM varchar(500), VAL varchar(500) not null, CS_VER_PID bigint, CONCEPT_PID bigint, primary key (PID))")
+			.addSql(DriverTypeEnum.DERBY_EMBEDDED, "alter table TRM_CONCEPT_DESIG add constraint FK_CONCEPTDESIG_CSV foreign key (CS_VER_PID) references TRM_CODESYSTEM_VER")
+			.addSql(DriverTypeEnum.DERBY_EMBEDDED, "alter table TRM_CONCEPT_DESIG add constraint FK_CONCEPTDESIG_CONCEPT foreign key (CONCEPT_PID) references TRM_CONCEPT")
+			.addSql(DriverTypeEnum.MYSQL_5_7, "create table TRM_CONCEPT_DESIG (PID bigint not null, LANG varchar(500), USE_CODE varchar(500), USE_DISPLAY varchar(500), USE_SYSTEM varchar(500), VAL varchar(500) not null, CS_VER_PID bigint, CONCEPT_PID bigint, primary key (PID)) ENGINE=InnoDB")
+			.addSql(DriverTypeEnum.MYSQL_5_7, "alter table TRM_CONCEPT_DESIG add constraint FK_CONCEPTDESIG_CSV foreign key (CS_VER_PID) references TRM_CODESYSTEM_VER (PID)")
+			.addSql(DriverTypeEnum.MYSQL_5_7, "alter table TRM_CONCEPT_DESIG add constraint FK_CONCEPTDESIG_CONCEPT foreign key (CONCEPT_PID) references TRM_CONCEPT (PID)")
+			.addSql(DriverTypeEnum.MARIADB_10_1, "create table TRM_CONCEPT_DESIG (PID bigint not null, LANG varchar(500), USE_CODE varchar(500), USE_DISPLAY varchar(500), USE_SYSTEM varchar(500), VAL varchar(500) not null, CS_VER_PID bigint, CONCEPT_PID bigint, primary key (PID))")
+			.addSql(DriverTypeEnum.MARIADB_10_1, "alter table TRM_CONCEPT_DESIG add constraint FK_CONCEPTDESIG_CSV foreign key (CS_VER_PID) references TRM_CODESYSTEM_VER (PID)")
+			.addSql(DriverTypeEnum.MARIADB_10_1, "alter table TRM_CONCEPT_DESIG add constraint FK_CONCEPTDESIG_CONCEPT foreign key (CONCEPT_PID) references TRM_CONCEPT (PID)")
+			.addSql(DriverTypeEnum.ORACLE_12C, "create table TRM_CONCEPT_DESIG (PID number(19,0) not null, LANG varchar2(500 char), USE_CODE varchar2(500 char), USE_DISPLAY varchar2(500 char), USE_SYSTEM varchar2(500 char), VAL varchar2(500 char) not null, CS_VER_PID number(19,0), CONCEPT_PID number(19,0), primary key (PID))")
+			.addSql(DriverTypeEnum.ORACLE_12C, "alter table TRM_CONCEPT_DESIG add constraint FK_CONCEPTDESIG_CSV foreign key (CS_VER_PID) references TRM_CODESYSTEM_VER")
+			.addSql(DriverTypeEnum.ORACLE_12C, "alter table TRM_CONCEPT_DESIG add constraint FK_CONCEPTDESIG_CONCEPT foreign key (CONCEPT_PID) references TRM_CONCEPT")
+			.addSql(DriverTypeEnum.POSTGRES_9_4, "create table TRM_CONCEPT_DESIG (PID int8 not null, LANG varchar(500), USE_CODE varchar(500), USE_DISPLAY varchar(500), USE_SYSTEM varchar(500), VAL varchar(500) not null, CS_VER_PID int8, CONCEPT_PID int8, primary key (PID))")
+			.addSql(DriverTypeEnum.POSTGRES_9_4, "alter table TRM_CONCEPT_DESIG add constraint FK_CONCEPTDESIG_CSV foreign key (CS_VER_PID) references TRM_CODESYSTEM_VER")
+			.addSql(DriverTypeEnum.POSTGRES_9_4, "alter table TRM_CONCEPT_DESIG add constraint FK_CONCEPTDESIG_CONCEPT foreign key (CONCEPT_PID) references TRM_CONCEPT")
+			.addSql(DriverTypeEnum.MSSQL_2012, "create table TRM_CONCEPT_DESIG (PID bigint not null, LANG varchar(500), USE_CODE varchar(500), USE_DISPLAY varchar(500), USE_SYSTEM varchar(500), VAL varchar(500) not null, CS_VER_PID bigint, CONCEPT_PID bigint, primary key (PID))")
+			.addSql(DriverTypeEnum.MSSQL_2012, "alter table TRM_CONCEPT_DESIG add constraint FK_CONCEPTDESIG_CSV foreign key (CS_VER_PID) references TRM_CODESYSTEM_VER")
+			.addSql(DriverTypeEnum.MSSQL_2012, "alter table TRM_CONCEPT_DESIG add constraint FK_CONCEPTDESIG_CONCEPT foreign key (CONCEPT_PID) references TRM_CONCEPT");
+
+		// Concept Property
+		version.startSectionWithMessage("Starting work on table: TRM_CONCEPT_PROPERTY");
+		version
+			.addTable("TRM_CONCEPT_PROPERTY")
+			.addSql(DriverTypeEnum.DERBY_EMBEDDED, "create table TRM_CONCEPT_PROPERTY (PID bigint not null, PROP_CODESYSTEM varchar(500), PROP_DISPLAY varchar(500), PROP_KEY varchar(500) not null, PROP_TYPE integer not null, PROP_VAL varchar(500), CS_VER_PID bigint, CONCEPT_PID bigint, primary key (PID))")
+			.addSql(DriverTypeEnum.DERBY_EMBEDDED, "alter table TRM_CONCEPT_PROPERTY add constraint FK_CONCEPTPROP_CSV foreign key (CS_VER_PID) references TRM_CODESYSTEM_VER")
+			.addSql(DriverTypeEnum.DERBY_EMBEDDED, "alter table TRM_CONCEPT_PROPERTY add constraint FK_CONCEPTPROP_CONCEPT foreign key (CONCEPT_PID) references TRM_CONCEPT")
+			.addSql(DriverTypeEnum.MARIADB_10_1, "create table TRM_CONCEPT_PROPERTY (PID bigint not null, PROP_CODESYSTEM varchar(500), PROP_DISPLAY varchar(500), PROP_KEY varchar(500) not null, PROP_TYPE integer not null, PROP_VAL varchar(500), CS_VER_PID bigint, CONCEPT_PID bigint, primary key (PID))")
+			.addSql(DriverTypeEnum.MARIADB_10_1, "alter table TRM_CONCEPT_PROPERTY add constraint FK_CONCEPTPROP_CSV foreign key (CS_VER_PID) references TRM_CODESYSTEM_VER (PID)")
+			.addSql(DriverTypeEnum.MARIADB_10_1, "alter table TRM_CONCEPT_PROPERTY add constraint FK_CONCEPTPROP_CONCEPT foreign key (CONCEPT_PID) references TRM_CONCEPT (PID)")
+			.addSql(DriverTypeEnum.MYSQL_5_7, "create table TRM_CONCEPT_PROPERTY (PID bigint not null, PROP_CODESYSTEM varchar(500), PROP_DISPLAY varchar(500), PROP_KEY varchar(500) not null, PROP_TYPE integer not null, PROP_VAL varchar(500), CS_VER_PID bigint, CONCEPT_PID bigint, primary key (PID))")
+			.addSql(DriverTypeEnum.MYSQL_5_7, "alter table TRM_CONCEPT_PROPERTY add constraint FK_CONCEPTPROP_CSV foreign key (CS_VER_PID) references TRM_CODESYSTEM_VER (PID)")
+			.addSql(DriverTypeEnum.MYSQL_5_7, "alter table TRM_CONCEPT_PROPERTY add constraint FK_CONCEPTPROP_CONCEPT foreign key (CONCEPT_PID) references TRM_CONCEPT (PID)")
+			.addSql(DriverTypeEnum.ORACLE_12C, "create table TRM_CONCEPT_PROPERTY (PID number(19,0) not null, PROP_CODESYSTEM varchar2(500 char), PROP_DISPLAY varchar2(500 char), PROP_KEY varchar2(500 char) not null, PROP_TYPE number(10,0) not null, PROP_VAL varchar2(500 char), CS_VER_PID number(19,0), CONCEPT_PID number(19,0), primary key (PID))")
+			.addSql(DriverTypeEnum.ORACLE_12C, "alter table TRM_CONCEPT_PROPERTY add constraint FK_CONCEPTPROP_CSV foreign key (CS_VER_PID) references TRM_CODESYSTEM_VER")
+			.addSql(DriverTypeEnum.ORACLE_12C, "alter table TRM_CONCEPT_PROPERTY add constraint FK_CONCEPTPROP_CONCEPT foreign key (CONCEPT_PID) references TRM_CONCEPT")
+			.addSql(DriverTypeEnum.POSTGRES_9_4, "create table TRM_CONCEPT_PROPERTY (PID int8 not null, PROP_CODESYSTEM varchar(500), PROP_DISPLAY varchar(500), PROP_KEY varchar(500) not null, PROP_TYPE int4 not null, PROP_VAL varchar(500), CS_VER_PID int8, CONCEPT_PID int8, primary key (PID))")
+			.addSql(DriverTypeEnum.POSTGRES_9_4, "alter table TRM_CONCEPT_PROPERTY add constraint FK_CONCEPTPROP_CSV foreign key (CS_VER_PID) references TRM_CODESYSTEM_VER")
+			.addSql(DriverTypeEnum.POSTGRES_9_4, "alter table TRM_CONCEPT_PROPERTY add constraint FK_CONCEPTPROP_CONCEPT foreign key (CONCEPT_PID) references TRM_CONCEPT")
+			.addSql(DriverTypeEnum.MSSQL_2012, "create table TRM_CONCEPT_PROPERTY (PID bigint not null, PROP_CODESYSTEM varchar(500), PROP_DISPLAY varchar(500), PROP_KEY varchar(500) not null, PROP_TYPE int not null, PROP_VAL varchar(500), CS_VER_PID bigint, CONCEPT_PID bigint, primary key (PID))")
+			.addSql(DriverTypeEnum.MSSQL_2012, "alter table TRM_CONCEPT_PROPERTY add constraint FK_CONCEPTPROP_CSV foreign key (CS_VER_PID) references TRM_CODESYSTEM_VER")
+			.addSql(DriverTypeEnum.MSSQL_2012, "alter table TRM_CONCEPT_PROPERTY add constraint FK_CONCEPTPROP_CONCEPT foreign key (CONCEPT_PID) references TRM_CONCEPT");
+
+		// Concept Map - Map
+		version.startSectionWithMessage("Starting work on table: TRM_CONCEPT_MAP");
+		version
+			.addTable("TRM_CONCEPT_MAP")
+			.addSql(DriverTypeEnum.DERBY_EMBEDDED, "create table TRM_CONCEPT_MAP (PID bigint not null, RES_ID bigint, SOURCE_URL varchar(200), TARGET_URL varchar(200), URL varchar(200) not null, primary key (PID))")
+			.addSql(DriverTypeEnum.DERBY_EMBEDDED, "alter table TRM_CONCEPT_MAP add constraint FK_TRMCONCEPTMAP_RES foreign key (RES_ID) references HFJ_RESOURCE")
+			.addSql(DriverTypeEnum.MYSQL_5_7, "create table TRM_CONCEPT_MAP (PID bigint not null, RES_ID bigint, SOURCE_URL varchar(200), TARGET_URL varchar(200), URL varchar(200) not null, primary key (PID))")
+			.addSql(DriverTypeEnum.MYSQL_5_7, "alter table TRM_CONCEPT_MAP add constraint IDX_CONCEPT_MAP_URL unique (URL)")
+			.addSql(DriverTypeEnum.MYSQL_5_7, "alter table TRM_CONCEPT_MAP add constraint FK_TRMCONCEPTMAP_RES foreign key (RES_ID) references HFJ_RESOURCE (RES_ID)")
+			.addSql(DriverTypeEnum.ORACLE_12C, "create table TRM_CONCEPT_MAP (PID number(19,0) not null, RES_ID number(19,0), SOURCE_URL varchar2(200 char), TARGET_URL varchar2(200 char), URL varchar2(200 char) not null, primary key (PID))")
+			.addSql(DriverTypeEnum.ORACLE_12C, "alter table TRM_CONCEPT_MAP add constraint IDX_CONCEPT_MAP_URL unique (URL)")
+			.addSql(DriverTypeEnum.ORACLE_12C, "alter table TRM_CONCEPT_MAP add constraint FK_TRMCONCEPTMAP_RES foreign key (RES_ID) references HFJ_RESOURCE")
+			.addSql(DriverTypeEnum.POSTGRES_9_4, "create table TRM_CONCEPT_MAP (PID int8 not null, RES_ID int8, SOURCE_URL varchar(200), TARGET_URL varchar(200), URL varchar(200) not null, primary key (PID))")
+			.addSql(DriverTypeEnum.POSTGRES_9_4, "alter table TRM_CONCEPT_MAP add constraint FK_TRMCONCEPTMAP_RES foreign key (RES_ID) references HFJ_RESOURCE")
+			.addSql(DriverTypeEnum.POSTGRES_9_4, "alter table TRM_CONCEPT_MAP add constraint IDX_CONCEPT_MAP_URL unique (URL)")
+			.addSql(DriverTypeEnum.MSSQL_2012, "create table TRM_CONCEPT_MAP (PID bigint not null, RES_ID bigint, SOURCE_URL varchar(200), TARGET_URL varchar(200), URL varchar(200) not null, primary key (PID))")
+			.addSql(DriverTypeEnum.MSSQL_2012, "alter table TRM_CONCEPT_MAP add constraint IDX_CONCEPT_MAP_URL unique (URL)")
+			.addSql(DriverTypeEnum.MSSQL_2012, "alter table TRM_CONCEPT_MAP add constraint FK_TRMCONCEPTMAP_RES foreign key (RES_ID) references HFJ_RESOURCE")
+			.addSql(DriverTypeEnum.MARIADB_10_1, "create table TRM_CONCEPT_MAP (PID bigint not null, RES_ID bigint, SOURCE_URL varchar(200), TARGET_URL varchar(200), URL varchar(200) not null, primary key (PID))")
+			.addSql(DriverTypeEnum.MARIADB_10_1, "alter table TRM_CONCEPT_MAP add constraint FK_TRMCONCEPTMAP_RES foreign key (RES_ID) references HFJ_RESOURCE (RES_ID)")
+			.addSql(DriverTypeEnum.MARIADB_10_1, "alter table TRM_CONCEPT_MAP add constraint IDX_CONCEPT_MAP_URL unique (URL)");
+
+		// Concept Map - Group
+		version.startSectionWithMessage("Starting work on table: TRM_CONCEPT_MAP_GROUP");
+		version
+			.addTable("TRM_CONCEPT_MAP_GROUP")
+			.addSql(DriverTypeEnum.DERBY_EMBEDDED, "create table TRM_CONCEPT_MAP_GROUP (PID bigint not null, myConceptMapUrl varchar(255), SOURCE_URL varchar(200) not null, mySourceValueSet varchar(255), SOURCE_VERSION varchar(100), TARGET_URL varchar(200) not null, myTargetValueSet varchar(255), TARGET_VERSION varchar(100), CONCEPT_MAP_PID bigint not null, primary key (PID))")
+			.addSql(DriverTypeEnum.DERBY_EMBEDDED, "alter table TRM_CONCEPT_MAP_GROUP add constraint FK_TCMGROUP_CONCEPTMAP foreign key (CONCEPT_MAP_PID) references TRM_CONCEPT_MAP")
+			.addSql(DriverTypeEnum.DERBY_EMBEDDED, "create unique index IDX_CONCEPT_MAP_URL on TRM_CONCEPT_MAP (URL)")
+			.addSql(DriverTypeEnum.ORACLE_12C, "create table TRM_CONCEPT_MAP_GROUP (PID number(19,0) not null, myConceptMapUrl varchar2(255 char), SOURCE_URL varchar2(200 char) not null, mySourceValueSet varchar2(255 char), SOURCE_VERSION varchar2(100 char), TARGET_URL varchar2(200 char) not null, myTargetValueSet varchar2(255 char), TARGET_VERSION varchar2(100 char), CONCEPT_MAP_PID number(19,0) not null, primary key (PID))")
+			.addSql(DriverTypeEnum.ORACLE_12C, "alter table TRM_CONCEPT_MAP_GROUP add constraint FK_TCMGROUP_CONCEPTMAP foreign key (CONCEPT_MAP_PID) references TRM_CONCEPT_MAP")
+			.addSql(DriverTypeEnum.MARIADB_10_1, "create table TRM_CONCEPT_MAP_GROUP (PID bigint not null, myConceptMapUrl varchar(255), SOURCE_URL varchar(200) not null, mySourceValueSet varchar(255), SOURCE_VERSION varchar(100), TARGET_URL varchar(200) not null, myTargetValueSet varchar(255), TARGET_VERSION varchar(100), CONCEPT_MAP_PID bigint not null, primary key (PID))")
+			.addSql(DriverTypeEnum.MARIADB_10_1, "alter table TRM_CONCEPT_MAP_GROUP add constraint FK_TCMGROUP_CONCEPTMAP foreign key (CONCEPT_MAP_PID) references TRM_CONCEPT_MAP (PID)")
+			.addSql(DriverTypeEnum.MYSQL_5_7, "create table TRM_CONCEPT_MAP_GROUP (PID bigint not null, myConceptMapUrl varchar(255), SOURCE_URL varchar(200) not null, mySourceValueSet varchar(255), SOURCE_VERSION varchar(100), TARGET_URL varchar(200) not null, myTargetValueSet varchar(255), TARGET_VERSION varchar(100), CONCEPT_MAP_PID bigint not null, primary key (PID))")
+			.addSql(DriverTypeEnum.MYSQL_5_7, "alter table TRM_CONCEPT_MAP_GROUP add constraint FK_TCMGROUP_CONCEPTMAP foreign key (CONCEPT_MAP_PID) references TRM_CONCEPT_MAP (PID)")
+			.addSql(DriverTypeEnum.MSSQL_2012, "create table TRM_CONCEPT_MAP_GROUP (PID bigint not null, myConceptMapUrl varchar(255), SOURCE_URL varchar(200) not null, mySourceValueSet varchar(255), SOURCE_VERSION varchar(100), TARGET_URL varchar(200) not null, myTargetValueSet varchar(255), TARGET_VERSION varchar(100), CONCEPT_MAP_PID bigint not null, primary key (PID))")
+			.addSql(DriverTypeEnum.MSSQL_2012, "alter table TRM_CONCEPT_MAP_GROUP add constraint FK_TCMGROUP_CONCEPTMAP foreign key (CONCEPT_MAP_PID) references TRM_CONCEPT_MAP")
+			.addSql(DriverTypeEnum.POSTGRES_9_4, "create table TRM_CONCEPT_MAP_GROUP (PID int8 not null, myConceptMapUrl varchar(255), SOURCE_URL varchar(200) not null, mySourceValueSet varchar(255), SOURCE_VERSION varchar(100), TARGET_URL varchar(200) not null, myTargetValueSet varchar(255), TARGET_VERSION varchar(100), CONCEPT_MAP_PID int8 not null, primary key (PID))")
+			.addSql(DriverTypeEnum.POSTGRES_9_4, "alter table TRM_CONCEPT_MAP_GROUP add constraint FK_TCMGROUP_CONCEPTMAP foreign key (CONCEPT_MAP_PID) references TRM_CONCEPT_MAP");
+
+		// Concept Map - Group Element
+		version.startSectionWithMessage("Starting work on table: TRM_CONCEPT_MAP_GRP_ELEMENT");
+		version
+			.addTable("TRM_CONCEPT_MAP_GRP_ELEMENT")
+			.addSql(DriverTypeEnum.DERBY_EMBEDDED, "create table TRM_CONCEPT_MAP_GRP_ELEMENT (PID bigint not null, SOURCE_CODE varchar(500) not null, myConceptMapUrl varchar(255), SOURCE_DISPLAY varchar(400), mySystem varchar(255), mySystemVersion varchar(255), myValueSet varchar(255), CONCEPT_MAP_GROUP_PID bigint not null, primary key (PID))")
+			.addSql(DriverTypeEnum.DERBY_EMBEDDED, "alter table TRM_CONCEPT_MAP_GRP_ELEMENT add constraint FK_TCMGELEMENT_GROUP foreign key (CONCEPT_MAP_GROUP_PID) references TRM_CONCEPT_MAP_GROUP")
+			.addSql(DriverTypeEnum.MARIADB_10_1, "create table TRM_CONCEPT_MAP_GRP_ELEMENT (PID bigint not null, SOURCE_CODE varchar(500) not null, myConceptMapUrl varchar(255), SOURCE_DISPLAY varchar(400), mySystem varchar(255), mySystemVersion varchar(255), myValueSet varchar(255), CONCEPT_MAP_GROUP_PID bigint not null, primary key (PID))")
+			.addSql(DriverTypeEnum.MARIADB_10_1, "alter table TRM_CONCEPT_MAP_GRP_ELEMENT add constraint FK_TCMGELEMENT_GROUP foreign key (CONCEPT_MAP_GROUP_PID) references TRM_CONCEPT_MAP_GROUP (PID)")
+			.addSql(DriverTypeEnum.MARIADB_10_1, "create index IDX_CNCPT_MAP_GRP_CD on TRM_CONCEPT_MAP_GRP_ELEMENT (SOURCE_CODE)")
+			.addSql(DriverTypeEnum.DERBY_EMBEDDED, "create index IDX_CNCPT_MAP_GRP_CD on TRM_CONCEPT_MAP_GRP_ELEMENT (SOURCE_CODE)")
+			.addSql(DriverTypeEnum.MYSQL_5_7, "create table TRM_CONCEPT_MAP_GRP_ELEMENT (PID bigint not null, SOURCE_CODE varchar(500) not null, myConceptMapUrl varchar(255), SOURCE_DISPLAY varchar(400), mySystem varchar(255), mySystemVersion varchar(255), myValueSet varchar(255), CONCEPT_MAP_GROUP_PID bigint not null, primary key (PID))")
+			.addSql(DriverTypeEnum.MYSQL_5_7, "create index IDX_CNCPT_MAP_GRP_CD on TRM_CONCEPT_MAP_GRP_ELEMENT (SOURCE_CODE)")
+			.addSql(DriverTypeEnum.MYSQL_5_7, "alter table TRM_CONCEPT_MAP_GRP_ELEMENT add constraint FK_TCMGELEMENT_GROUP foreign key (CONCEPT_MAP_GROUP_PID) references TRM_CONCEPT_MAP_GROUP (PID)")
+			.addSql(DriverTypeEnum.POSTGRES_9_4, "create table TRM_CONCEPT_MAP_GRP_ELEMENT (PID int8 not null, SOURCE_CODE varchar(500) not null, myConceptMapUrl varchar(255), SOURCE_DISPLAY varchar(400), mySystem varchar(255), mySystemVersion varchar(255), myValueSet varchar(255), CONCEPT_MAP_GROUP_PID int8 not null, primary key (PID))")
+			.addSql(DriverTypeEnum.POSTGRES_9_4, "alter table TRM_CONCEPT_MAP_GRP_ELEMENT add constraint FK_TCMGELEMENT_GROUP foreign key (CONCEPT_MAP_GROUP_PID) references TRM_CONCEPT_MAP_GROUP")
+			.addSql(DriverTypeEnum.POSTGRES_9_4, "create index IDX_CNCPT_MAP_GRP_CD on TRM_CONCEPT_MAP_GRP_ELEMENT (SOURCE_CODE)")
+			.addSql(DriverTypeEnum.ORACLE_12C, "create table TRM_CONCEPT_MAP_GRP_ELEMENT (PID number(19,0) not null, SOURCE_CODE varchar2(500 char) not null, myConceptMapUrl varchar2(255 char), SOURCE_DISPLAY varchar2(400 char), mySystem varchar2(255 char), mySystemVersion varchar2(255 char), myValueSet varchar2(255 char), CONCEPT_MAP_GROUP_PID number(19,0) not null, primary key (PID))")
+			.addSql(DriverTypeEnum.ORACLE_12C, "alter table TRM_CONCEPT_MAP_GRP_ELEMENT add constraint FK_TCMGELEMENT_GROUP foreign key (CONCEPT_MAP_GROUP_PID) references TRM_CONCEPT_MAP_GROUP")
+			.addSql(DriverTypeEnum.ORACLE_12C, "create index IDX_CNCPT_MAP_GRP_CD on TRM_CONCEPT_MAP_GRP_ELEMENT (SOURCE_CODE)")
+			.addSql(DriverTypeEnum.MSSQL_2012, "create table TRM_CONCEPT_MAP_GRP_ELEMENT (PID bigint not null, SOURCE_CODE varchar(500) not null, myConceptMapUrl varchar(255), SOURCE_DISPLAY varchar(400), mySystem varchar(255), mySystemVersion varchar(255), myValueSet varchar(255), CONCEPT_MAP_GROUP_PID bigint not null, primary key (PID))")
+			.addSql(DriverTypeEnum.MSSQL_2012, "create index IDX_CNCPT_MAP_GRP_CD on TRM_CONCEPT_MAP_GRP_ELEMENT (SOURCE_CODE)")
+			.addSql(DriverTypeEnum.MSSQL_2012, "alter table TRM_CONCEPT_MAP_GRP_ELEMENT add constraint FK_TCMGELEMENT_GROUP foreign key (CONCEPT_MAP_GROUP_PID) references TRM_CONCEPT_MAP_GROUP");
+
+		// Concept Map - Group Element Target
+		version.startSectionWithMessage("Starting work on table: TRM_CONCEPT_MAP_GRP_ELM_TGT");
+		version
+			.addTable("TRM_CONCEPT_MAP_GRP_ELM_TGT")
+			.addSql(DriverTypeEnum.DERBY_EMBEDDED, "create table TRM_CONCEPT_MAP_GRP_ELM_TGT (PID bigint not null, TARGET_CODE varchar(500) not null, myConceptMapUrl varchar(255), TARGET_DISPLAY varchar(400), TARGET_EQUIVALENCE varchar(50), mySystem varchar(255), mySystemVersion varchar(255), myValueSet varchar(255), CONCEPT_MAP_GRP_ELM_PID bigint not null, primary key (PID))")
+			.addSql(DriverTypeEnum.DERBY_EMBEDDED, "alter table TRM_CONCEPT_MAP_GRP_ELM_TGT add constraint FK_TCMGETARGET_ELEMENT foreign key (CONCEPT_MAP_GRP_ELM_PID) references TRM_CONCEPT_MAP_GRP_ELEMENT")
+			.addSql(DriverTypeEnum.DERBY_EMBEDDED, "create index IDX_CNCPT_MP_GRP_ELM_TGT_CD on TRM_CONCEPT_MAP_GRP_ELM_TGT (TARGET_CODE)")
+			.addSql(DriverTypeEnum.MARIADB_10_1, "create table TRM_CONCEPT_MAP_GRP_ELM_TGT (PID bigint not null, TARGET_CODE varchar(500) not null, myConceptMapUrl varchar(255), TARGET_DISPLAY varchar(400), TARGET_EQUIVALENCE varchar(50), mySystem varchar(255), mySystemVersion varchar(255), myValueSet varchar(255), CONCEPT_MAP_GRP_ELM_PID bigint not null, primary key (PID))")
+			.addSql(DriverTypeEnum.MARIADB_10_1, "alter table TRM_CONCEPT_MAP_GRP_ELM_TGT add constraint FK_TCMGETARGET_ELEMENT foreign key (CONCEPT_MAP_GRP_ELM_PID) references TRM_CONCEPT_MAP_GRP_ELEMENT (PID)")
+			.addSql(DriverTypeEnum.MARIADB_10_1, "create index IDX_CNCPT_MP_GRP_ELM_TGT_CD on TRM_CONCEPT_MAP_GRP_ELM_TGT (TARGET_CODE)")
+			.addSql(DriverTypeEnum.MYSQL_5_7, "create table TRM_CONCEPT_MAP_GRP_ELM_TGT (PID bigint not null, TARGET_CODE varchar(500) not null, myConceptMapUrl varchar(255), TARGET_DISPLAY varchar(400), TARGET_EQUIVALENCE varchar(50), mySystem varchar(255), mySystemVersion varchar(255), myValueSet varchar(255), CONCEPT_MAP_GRP_ELM_PID bigint not null, primary key (PID))")
+			.addSql(DriverTypeEnum.MYSQL_5_7, "alter table TRM_CONCEPT_MAP_GRP_ELM_TGT add constraint FK_TCMGETARGET_ELEMENT foreign key (CONCEPT_MAP_GRP_ELM_PID) references TRM_CONCEPT_MAP_GRP_ELEMENT (PID)")
+			.addSql(DriverTypeEnum.MYSQL_5_7, "create index IDX_CNCPT_MP_GRP_ELM_TGT_CD on TRM_CONCEPT_MAP_GRP_ELM_TGT (TARGET_CODE)")
+			.addSql(DriverTypeEnum.ORACLE_12C, "create table TRM_CONCEPT_MAP_GRP_ELM_TGT (PID number(19,0) not null, TARGET_CODE varchar2(500 char) not null, myConceptMapUrl varchar2(255 char), TARGET_DISPLAY varchar2(400 char), TARGET_EQUIVALENCE varchar2(50 char), mySystem varchar2(255 char), mySystemVersion varchar2(255 char), myValueSet varchar2(255 char), CONCEPT_MAP_GRP_ELM_PID number(19,0) not null, primary key (PID))")
+			.addSql(DriverTypeEnum.ORACLE_12C, "alter table TRM_CONCEPT_MAP_GRP_ELM_TGT add constraint FK_TCMGETARGET_ELEMENT foreign key (CONCEPT_MAP_GRP_ELM_PID) references TRM_CONCEPT_MAP_GRP_ELEMENT")
+			.addSql(DriverTypeEnum.ORACLE_12C, "create index IDX_CNCPT_MP_GRP_ELM_TGT_CD on TRM_CONCEPT_MAP_GRP_ELM_TGT (TARGET_CODE)")
+			.addSql(DriverTypeEnum.POSTGRES_9_4, "create table TRM_CONCEPT_MAP_GRP_ELM_TGT (PID int8 not null, TARGET_CODE varchar(500) not null, myConceptMapUrl varchar(255), TARGET_DISPLAY varchar(400), TARGET_EQUIVALENCE varchar(50), mySystem varchar(255), mySystemVersion varchar(255), myValueSet varchar(255), CONCEPT_MAP_GRP_ELM_PID int8 not null, primary key (PID))")
+			.addSql(DriverTypeEnum.POSTGRES_9_4, "alter table TRM_CONCEPT_MAP_GRP_ELM_TGT add constraint FK_TCMGETARGET_ELEMENT foreign key (CONCEPT_MAP_GRP_ELM_PID) references TRM_CONCEPT_MAP_GRP_ELEMENT")
+			.addSql(DriverTypeEnum.POSTGRES_9_4, "create index IDX_CNCPT_MP_GRP_ELM_TGT_CD on TRM_CONCEPT_MAP_GRP_ELM_TGT (TARGET_CODE)")
+			.addSql(DriverTypeEnum.MSSQL_2012, "create table TRM_CONCEPT_MAP_GRP_ELM_TGT (PID bigint not null, TARGET_CODE varchar(500) not null, myConceptMapUrl varchar(255), TARGET_DISPLAY varchar(400), TARGET_EQUIVALENCE varchar(50), mySystem varchar(255), mySystemVersion varchar(255), myValueSet varchar(255), CONCEPT_MAP_GRP_ELM_PID bigint not null, primary key (PID))")
+			.addSql(DriverTypeEnum.MSSQL_2012, "create index IDX_CNCPT_MP_GRP_ELM_TGT_CD on TRM_CONCEPT_MAP_GRP_ELM_TGT (TARGET_CODE)")
+			.addSql(DriverTypeEnum.MSSQL_2012, "alter table TRM_CONCEPT_MAP_GRP_ELM_TGT add constraint FK_TCMGETARGET_ELEMENT foreign key (CONCEPT_MAP_GRP_ELM_PID) references TRM_CONCEPT_MAP_GRP_ELEMENT");
+	}
+
+
+}

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/api/BaseMigrationTasks.java

@@ -0,0 +1,203 @@
+package ca.uhn.fhir.jpa.migrate.tasks.api;
+
+import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
+import ca.uhn.fhir.jpa.migrate.taskdef.*;
+import ca.uhn.fhir.jpa.migrate.tasks.HapiFhirJpaMigrationTasks;
+import ca.uhn.fhir.util.VersionEnum;
+import com.google.common.collect.Multimap;
+import com.google.common.collect.MultimapBuilder;
+import org.apache.commons.lang3.Validate;
+import org.intellij.lang.annotations.Language;
+
+import javax.annotation.Nonnull;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+public class BaseMigrationTasks {
+	private Multimap<VersionEnum, BaseTask<?>> myTasks = MultimapBuilder.hashKeys().arrayListValues().build();
+
+	public List<BaseTask<?>> getTasks(@Nonnull VersionEnum theFrom, @Nonnull VersionEnum theTo) {
+		Validate.notNull(theFrom);
+		Validate.notNull(theTo);
+		Validate.isTrue(theFrom.ordinal() < theTo.ordinal(), "From version must be lower than to version");
+
+		List<BaseTask<?>> retVal = new ArrayList<>();
+		for (VersionEnum nextVersion : VersionEnum.values()) {
+			if (nextVersion.ordinal() <= theFrom.ordinal()) {
+				continue;
+			}
+			if (nextVersion.ordinal() > theTo.ordinal()) {
+				continue;
+			}
+
+			Collection<BaseTask<?>> nextValues = myTasks.get(nextVersion);
+			if (nextValues != null) {
+				retVal.addAll(nextValues);
+			}
+		}
+
+		return retVal;
+	}
+
+	protected HapiFhirJpaMigrationTasks.Builder forVersion(VersionEnum theVersion) {
+		return new HapiFhirJpaMigrationTasks.Builder(theVersion);
+	}
+
+	protected class Builder {
+
+		private final VersionEnum myVersion;
+		private String myTableName;
+
+		Builder(VersionEnum theVersion) {
+			myVersion = theVersion;
+		}
+
+		public BuilderWithTableName onTable(String theTableName) {
+			myTableName = theTableName;
+			return new BuilderWithTableName();
+		}
+
+		public void addTask(BaseTask theTask) {
+			theTask.validate();
+			myTasks.put(myVersion, theTask);
+		}
+
+		public BuilderAddTable addTable(String theTableName) {
+			myTableName = theTableName;
+			return new BuilderAddTable();
+		}
+
+		public void startSectionWithMessage(String theMessage) {
+			Validate.notBlank(theMessage);
+			addTask(new LogStartSectionWithMessageTask(theMessage));
+		}
+
+		public class BuilderWithTableName {
+			private String myIndexName;
+			private String myColumnName;
+
+			public String getTableName() {
+				return myTableName;
+			}
+
+			public void dropIndex(String theIndexName) {
+				DropIndexTask task = new DropIndexTask();
+				task.setIndexName(theIndexName);
+				task.setTableName(myTableName);
+				addTask(task);
+			}
+
+			public BuilderAddIndexWithName addIndex(String theIndexName) {
+				myIndexName = theIndexName;
+				return new BuilderAddIndexWithName();
+			}
+
+			public BuilderAddColumnWithName addColumn(String theColumnName) {
+				myColumnName = theColumnName;
+				return new BuilderAddColumnWithName();
+			}
+
+			public void addTask(BaseTableTask<?> theTask) {
+				theTask.setTableName(myTableName);
+				Builder.this.addTask(theTask);
+			}
+
+			public BuilderModifyColumnWithName modifyColumn(String theColumnName) {
+				myColumnName = theColumnName;
+				return new BuilderModifyColumnWithName();
+			}
+
+			public class BuilderAddIndexWithName {
+				private boolean myUnique;
+
+				public BuilderAddIndexUnique unique(boolean theUnique) {
+					myUnique = theUnique;
+					return new BuilderAddIndexUnique();
+				}
+
+				public class BuilderAddIndexUnique {
+					public void withColumns(String... theColumnNames) {
+						AddIndexTask task = new AddIndexTask();
+						task.setTableName(myTableName);
+						task.setIndexName(myIndexName);
+						task.setUnique(myUnique);
+						task.setColumns(theColumnNames);
+						addTask(task);
+					}
+				}
+			}
+
+			public class BuilderAddColumnWithName {
+				private boolean myNullable;
+
+				public BuilderAddColumnWithNameNullable nullable() {
+					myNullable = true;
+					return new BuilderAddColumnWithNameNullable();
+				}
+
+				public class BuilderAddColumnWithNameNullable {
+					public void type(AddColumnTask.ColumnTypeEnum theColumnType) {
+						AddColumnTask task = new AddColumnTask();
+						task.setColumnName(myColumnName);
+						task.setNullable(myNullable);
+						task.setColumnType(theColumnType);
+						addTask(task);
+					}
+				}
+			}
+
+			public class BuilderModifyColumnWithName {
+
+				private boolean myNullable;
+
+				public BuilderModifyColumnWithNameAndNullable nullable() {
+					myNullable = true;
+					return new BuilderModifyColumnWithNameAndNullable();
+				}
+
+				public BuilderModifyColumnWithNameAndNullable nonNullable() {
+					myNullable = false;
+					return new BuilderModifyColumnWithNameAndNullable();
+				}
+
+				public class BuilderModifyColumnWithNameAndNullable {
+
+					public void withType(BaseTableColumnTypeTask.ColumnTypeEnum theColumnType, int theLength) {
+						if (theColumnType == BaseTableColumnTypeTask.ColumnTypeEnum.STRING) {
+							ModifyColumnTask task = new ModifyColumnTask();
+							task.setColumnName(myColumnName);
+							task.setTableName(myTableName);
+							task.setColumnLength(theLength);
+							task.setNullable(myNullable);
+							task.setColumnType(theColumnType);
+							addTask(task);
+						} else {
+							throw new IllegalArgumentException("Can not specify length for column of type " + theColumnType);
+						}
+					}
+
+				}
+			}
+		}
+
+		public class BuilderAddTable {
+
+			private final AddTableTask myTask;
+
+			protected BuilderAddTable() {
+				myTask = new AddTableTask();
+				myTask.setTableName(myTableName);
+				addTask(myTask);
+			}
+
+
+			public BuilderAddTable addSql(DriverTypeEnum theDriverTypeEnum, @Language("SQL") String theSql) {
+				myTask.addSql(theDriverTypeEnum, theSql);
+				return this;
+			}
+		}
+	}
+
+
+}

hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/AddColumnTest.java

@@ -0,0 +1,44 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.jpa.migrate.JdbcUtils;
+import org.junit.Test;
+
+import java.sql.SQLException;
+
+import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.junit.Assert.assertThat;
+
+public class AddColumnTest extends BaseTest {
+
+	@Test
+	public void testColumnDoesntAlreadyExist() throws SQLException {
+		executeSql("create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255))");
+
+		AddColumnTask task = new AddColumnTask();
+		task.setTableName("SOMETABLE");
+		task.setColumnName("newcol");
+		task.setColumnType(AddColumnTask.ColumnTypeEnum.LONG);
+		task.setNullable(true);
+		getMigrator().addTask(task);
+
+		getMigrator().migrate();
+
+		assertThat(JdbcUtils.getColumnNames(getConnectionProperties(), "SOMETABLE"), containsInAnyOrder("PID", "TEXTCOL", "NEWCOL"));
+	}
+
+	@Test
+	public void testColumnAlreadyExists() throws SQLException {
+		executeSql("create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255), newcol bigint)");
+
+		AddColumnTask task = new AddColumnTask();
+		task.setTableName("SOMETABLE");
+		task.setColumnName("newcol");
+		task.setColumnType(AddColumnTask.ColumnTypeEnum.LONG);
+		getMigrator().addTask(task);
+
+		getMigrator().migrate();
+
+		assertThat(JdbcUtils.getColumnNames(getConnectionProperties(), "SOMETABLE"), containsInAnyOrder("PID", "TEXTCOL", "NEWCOL"));
+	}
+
+}

hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/AddIndexTest.java

@@ -0,0 +1,50 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.jpa.migrate.JdbcUtils;
+import com.google.common.collect.Lists;
+import org.junit.Test;
+
+import java.sql.SQLException;
+
+import static org.hamcrest.Matchers.contains;
+import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.junit.Assert.assertThat;
+
+public class AddIndexTest extends BaseTest {
+
+	@Test
+	public void testIndexAlreadyExists() throws SQLException {
+		executeSql("create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255))");
+		executeSql("create unique index IDX_ANINDEX on SOMETABLE (PID, TEXTCOL)");
+		executeSql("create unique index IDX_DIFINDEX on SOMETABLE (TEXTCOL)");
+
+		AddIndexTask task = new AddIndexTask();
+		task.setIndexName("IDX_ANINDEX");
+		task.setTableName("SOMETABLE");
+		task.setColumns("PID", "TEXTCOL");
+		task.setUnique(false);
+		getMigrator().addTask(task);
+
+		getMigrator().migrate();
+
+		assertThat(JdbcUtils.getIndexNames(getConnectionProperties(), "SOMETABLE"), containsInAnyOrder("IDX_DIFINDEX", "IDX_ANINDEX"));
+	}
+
+	@Test
+	public void testIndexDoesntAlreadyExist() throws SQLException {
+		executeSql("create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255))");
+		executeSql("create unique index IDX_DIFINDEX on SOMETABLE (TEXTCOL)");
+
+		AddIndexTask task = new AddIndexTask();
+		task.setIndexName("IDX_ANINDEX");
+		task.setTableName("SOMETABLE");
+		task.setColumns("PID", "TEXTCOL");
+		task.setUnique(false);
+		getMigrator().addTask(task);
+
+		getMigrator().migrate();
+
+		assertThat(JdbcUtils.getIndexNames(getConnectionProperties(), "SOMETABLE"), containsInAnyOrder("IDX_DIFINDEX", "IDX_ANINDEX"));
+	}
+
+}

hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/AddTableTest.java

@@ -0,0 +1,42 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
+import ca.uhn.fhir.jpa.migrate.JdbcUtils;
+import org.junit.Test;
+
+import java.sql.SQLException;
+
+import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.junit.Assert.assertThat;
+
+public class AddTableTest extends BaseTest {
+
+	@Test
+	public void testTableDoesntAlreadyExist() throws SQLException {
+
+		AddTableTask task = new AddTableTask();
+		task.setTableName("SOMETABLE");
+		task.addSql(DriverTypeEnum.DERBY_EMBEDDED, "create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255))");
+		getMigrator().addTask(task);
+
+		getMigrator().migrate();
+
+		assertThat(JdbcUtils.getTableNames(getConnectionProperties()), containsInAnyOrder("SOMETABLE"));
+	}
+
+	@Test
+	public void testTableAlreadyExists() throws SQLException {
+		executeSql("create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255))");
+		assertThat(JdbcUtils.getTableNames(getConnectionProperties()), containsInAnyOrder("SOMETABLE"));
+
+		AddTableTask task = new AddTableTask();
+		task.setTableName("SOMETABLE");
+		task.addSql(DriverTypeEnum.DERBY_EMBEDDED, "create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255))");
+		getMigrator().addTask(task);
+
+		getMigrator().migrate();
+
+		assertThat(JdbcUtils.getTableNames(getConnectionProperties()), containsInAnyOrder("SOMETABLE"));
+	}
+
+}

hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/ArbitrarySqlTest.java

@@ -0,0 +1,53 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.jpa.entity.SearchParamPresent;
+import org.junit.Test;
+
+import java.util.List;
+import java.util.Map;
+
+import static org.junit.Assert.assertEquals;
+
+public class ArbitrarySqlTest extends BaseTest {
+
+	@Test
+	public void test350MigrateSearchParams() {
+		executeSql("create table HFJ_SEARCH_PARM (PID bigint not null, RES_TYPE varchar(255), PARAM_NAME varchar(255))");
+		executeSql("insert into HFJ_SEARCH_PARM (PID, RES_TYPE, PARAM_NAME) values (1, 'Patient', 'identifier')");
+		executeSql("insert into HFJ_SEARCH_PARM (PID, RES_TYPE, PARAM_NAME) values (2, 'Patient', 'family')");
+		executeSql("create table HFJ_RES_PARAM_PRESENT (PID bigint, SP_ID bigint, SP_PRESENT boolean, HASH_PRESENT bigint)");
+		executeSql("insert into HFJ_RES_PARAM_PRESENT (PID, SP_ID, SP_PRESENT, HASH_PRESENT) values (100, 1, true, null)");
+		executeSql("insert into HFJ_RES_PARAM_PRESENT (PID, SP_ID, SP_PRESENT, HASH_PRESENT) values (101, 2, true, null)");
+
+		ArbitrarySqlTask task = new ArbitrarySqlTask("Consolidate search parameter presence indexes");
+		task.setBatchSize(1);
+		String sql = "SELECT " +
+			"HFJ_SEARCH_PARM.RES_TYPE RES_TYPE, HFJ_SEARCH_PARM.PARAM_NAME PARAM_NAME, " +
+			"HFJ_RES_PARAM_PRESENT.PID PID, HFJ_RES_PARAM_PRESENT.SP_ID SP_ID, HFJ_RES_PARAM_PRESENT.SP_PRESENT SP_PRESENT, HFJ_RES_PARAM_PRESENT.HASH_PRESENT HASH_PRESENT " +
+			"from HFJ_RES_PARAM_PRESENT " +
+			"join HFJ_SEARCH_PARM ON (HFJ_SEARCH_PARM.PID = HFJ_RES_PARAM_PRESENT.SP_ID) " +
+			"where HFJ_RES_PARAM_PRESENT.HASH_PRESENT is null";
+		task.addQuery(sql, ArbitrarySqlTask.QueryModeEnum.BATCH_UNTIL_NO_MORE, t -> {
+			Long pid = (Long) t.get("PID");
+			Boolean present = (Boolean) t.get("SP_PRESENT");
+			String resType = (String) t.get("RES_TYPE");
+			String paramName = (String) t.get("PARAM_NAME");
+			Long hash = SearchParamPresent.calculateHashPresence(resType, paramName, present);
+			task.executeSql("update HFJ_RES_PARAM_PRESENT set HASH_PRESENT = ? where PID = ?", hash, pid);
+		});
+
+		getMigrator().addTask(task);
+		getMigrator().migrate();
+
+
+		List<Map<String, Object>> rows = executeQuery("select * from HFJ_RES_PARAM_PRESENT order by PID asc");
+		assertEquals(2, rows.size());
+		assertEquals(100L, rows.get(0).get("PID"));
+		assertEquals(-1100208805056022671L, rows.get(0).get("HASH_PRESENT"));
+		assertEquals(101L, rows.get(1).get("PID"));
+		assertEquals(-756348509333838170L, rows.get(1).get("HASH_PRESENT"));
+
+	}
+
+
+}

hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseTest.java

@@ -0,0 +1,64 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
+import ca.uhn.fhir.jpa.migrate.Migrator;
+import org.intellij.lang.annotations.Language;
+import org.junit.After;
+import org.junit.Before;
+import org.springframework.jdbc.core.ColumnMapRowMapper;
+
+import java.util.List;
+import java.util.Map;
+
+public class BaseTest {
+
+	private static int ourDatabaseUrl = 0;
+	private String myUrl;
+	private Migrator myMigrator;
+	private DriverTypeEnum.ConnectionProperties myConnectionProperties;
+
+	public String getUrl() {
+		return myUrl;
+	}
+
+	public DriverTypeEnum.ConnectionProperties getConnectionProperties() {
+		return myConnectionProperties;
+	}
+
+
+	protected void executeSql(@Language("SQL") String theSql, Object... theArgs) {
+		myConnectionProperties.getTxTemplate().execute(t -> {
+			myConnectionProperties.newJdbcTemplate().update(theSql, theArgs);
+			return null;
+		});
+	}
+
+	protected List<Map<String, Object>> executeQuery(@Language("SQL") String theSql, Object... theArgs) {
+		return myConnectionProperties.getTxTemplate().execute(t -> {
+			return myConnectionProperties.newJdbcTemplate().query(theSql, theArgs, new ColumnMapRowMapper());
+		});
+	}
+
+	public Migrator getMigrator() {
+		return myMigrator;
+	}
+
+	@After
+	public void after() {
+		myConnectionProperties.close();
+	}
+
+	@Before()
+	public void before() {
+		myUrl = "jdbc:derby:memory:database " + (ourDatabaseUrl++) + ";create=true";
+
+		myConnectionProperties = DriverTypeEnum.DERBY_EMBEDDED.newConnectionProperties(myUrl, "SA", "SA");
+
+		myMigrator = new Migrator();
+		myMigrator.setConnectionUrl(myUrl);
+		myMigrator.setDriverType(DriverTypeEnum.DERBY_EMBEDDED);
+		myMigrator.setUsername("SA");
+		myMigrator.setPassword("SA");
+	}
+
+}

hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/CreateHashesTest.java

@@ -0,0 +1,53 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.jpa.entity.BaseResourceIndexedSearchParam;
+import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamToken;
+import org.junit.Test;
+import org.springframework.jdbc.core.JdbcTemplate;
+
+import java.util.Map;
+
+import static org.junit.Assert.assertEquals;
+
+public class CreateHashesTest extends BaseTest {
+
+	@Test
+	public void testCreateHashes() {
+		executeSql("create table HFJ_SPIDX_TOKEN (SP_ID bigint not null, SP_MISSING boolean, SP_NAME varchar(100) not null, RES_ID bigint, RES_TYPE varchar(255) not null, SP_UPDATED timestamp, HASH_IDENTITY bigint, HASH_SYS bigint, HASH_SYS_AND_VALUE bigint, HASH_VALUE bigint, SP_SYSTEM varchar(200), SP_VALUE varchar(200), primary key (SP_ID))");
+		executeSql("insert into HFJ_SPIDX_TOKEN (SP_MISSING, SP_NAME, RES_ID, RES_TYPE, SP_UPDATED, SP_SYSTEM, SP_VALUE, SP_ID) values (false, 'identifier', 999, 'Patient', '2018-09-03 07:44:49.196', 'urn:oid:1.2.410.100110.10.41308301', '88888888', 1)");
+		executeSql("insert into HFJ_SPIDX_TOKEN (SP_MISSING, SP_NAME, RES_ID, RES_TYPE, SP_UPDATED, SP_SYSTEM, SP_VALUE, SP_ID) values (false, 'identifier', 999, 'Patient', '2018-09-03 07:44:49.196', 'urn:oid:1.2.410.100110.10.41308301', '99999999', 2)");
+
+		CalculateHashesTask task = new CalculateHashesTask();
+		task.setTableName("HFJ_SPIDX_TOKEN");
+		task.setColumnName("HASH_IDENTITY");
+		task.addCalculator("HASH_IDENTITY", t -> BaseResourceIndexedSearchParam.calculateHashIdentity(t.getResourceType(), t.getString("SP_NAME")));
+		task.addCalculator("HASH_SYS", t -> ResourceIndexedSearchParamToken.calculateHashSystem(t.getResourceType(), t.getParamName(), t.getString("SP_SYSTEM")));
+		task.addCalculator("HASH_SYS_AND_VALUE", t -> ResourceIndexedSearchParamToken.calculateHashSystemAndValue(t.getResourceType(), t.getParamName(), t.getString("SP_SYSTEM"), t.getString("SP_VALUE")));
+		task.addCalculator("HASH_VALUE", t -> ResourceIndexedSearchParamToken.calculateHashValue(t.getResourceType(), t.getParamName(), t.getString("SP_VALUE")));
+		task.setBatchSize(1);
+		getMigrator().addTask(task);
+
+		getMigrator().migrate();
+
+
+		getConnectionProperties().getTxTemplate().execute(t -> {
+			Map<String, Object> map;
+			JdbcTemplate jdbcTemplate = getConnectionProperties().newJdbcTemplate();
+
+			map = jdbcTemplate.queryForMap("select * from HFJ_SPIDX_TOKEN where SP_ID = 1");
+			assertEquals(7001889285610424179L, map.get("HASH_IDENTITY"));
+			assertEquals(2686400398917843456L, map.get("HASH_SYS"));
+			assertEquals(-3943098850992523411L, map.get("HASH_SYS_AND_VALUE"));
+			assertEquals(845040519142030272L, map.get("HASH_VALUE"));
+
+			map = jdbcTemplate.queryForMap("select * from HFJ_SPIDX_TOKEN where SP_ID = 2");
+			assertEquals(7001889285610424179L, map.get("HASH_IDENTITY"));
+			assertEquals(2686400398917843456L, map.get("HASH_SYS"));
+			assertEquals(-6583685191951870327L, map.get("HASH_SYS_AND_VALUE"));
+			assertEquals(8271382783311609619L, map.get("HASH_VALUE"));
+
+			return null;
+		});
+	}
+
+}

hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/DropIndexTest.java

@@ -0,0 +1,46 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.jpa.migrate.JdbcUtils;
+import org.junit.Test;
+
+import java.sql.SQLException;
+
+import static org.hamcrest.Matchers.contains;
+import static org.junit.Assert.assertThat;
+
+public class DropIndexTest extends BaseTest {
+
+	@Test
+	public void testIndexAlreadyExists() throws SQLException {
+		executeSql("create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255))");
+		executeSql("create unique index IDX_ANINDEX on SOMETABLE (PID, TEXTCOL)");
+		executeSql("create unique index IDX_DIFINDEX on SOMETABLE (TEXTCOL)");
+
+		DropIndexTask task = new DropIndexTask();
+		task.setDescription("Drop an index");
+		task.setIndexName("IDX_ANINDEX");
+		task.setTableName("SOMETABLE");
+		getMigrator().addTask(task);
+
+		getMigrator().migrate();
+
+		assertThat(JdbcUtils.getIndexNames(getConnectionProperties(), "SOMETABLE"), contains("IDX_DIFINDEX"));
+	}
+
+	@Test
+	public void testIndexDoesntAlreadyExist() throws SQLException {
+		executeSql("create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255))");
+		executeSql("create unique index IDX_DIFINDEX on SOMETABLE (TEXTCOL)");
+
+		DropIndexTask task = new DropIndexTask();
+		task.setDescription("Drop an index");
+		task.setIndexName("IDX_ANINDEX");
+		task.setTableName("SOMETABLE");
+		getMigrator().addTask(task);
+
+		getMigrator().migrate();
+
+		assertThat(JdbcUtils.getIndexNames(getConnectionProperties(), "SOMETABLE"), contains("IDX_DIFINDEX"));
+	}
+
+}

hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/ModifyColumnTest.java

@@ -0,0 +1,32 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.jpa.migrate.JdbcUtils;
+import org.junit.Test;
+
+import java.sql.SQLException;
+
+import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
+
+public class ModifyColumnTest extends BaseTest {
+
+
+	@Test
+	public void testColumnAlreadyExists() throws SQLException {
+		executeSql("create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255), newcol bigint)");
+
+		ModifyColumnTask task = new ModifyColumnTask();
+		task.setTableName("SOMETABLE");
+		task.setColumnName("TEXTCOL");
+		task.setColumnType(AddColumnTask.ColumnTypeEnum.STRING);
+		task.setNullable(true);
+		task.setColumnLength(300);
+		getMigrator().addTask(task);
+
+		getMigrator().migrate();
+
+		assertEquals("varchar(300)", JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
+	}
+
+}

hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasksTest.java

@@ -0,0 +1,12 @@
+package ca.uhn.fhir.jpa.migrate.tasks;
+
+import org.junit.Test;
+
+public class HapiFhirJpaMigrationTasksTest {
+
+	@Test
+	public void testCreate() {
+		new HapiFhirJpaMigrationTasks();
+	}
+
+}

hapi-fhir-jpaserver-migrate/src/test/resources/logback-test.xml

@@ -0,0 +1,14 @@
+<configuration>
+
+	<appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
+		<encoder>
+			<pattern>%d{HH:mm:ss.SSS} [%thread] %-5level %logger{36} [%file:%line] - %msg%n
+			</pattern>
+		</encoder>
+	</appender>
+
+	<root level="info">
+		<appender-ref ref="STDOUT" />
+	</root>
+
+</configuration>

hapi-fhir-jpaserver-uhnfhirtest/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>3.5.0-SNAPSHOT</version>
+		<version>3.5.0</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 
@@ -158,7 +158,7 @@
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-converter</artifactId>
-			<version>3.5.0-SNAPSHOT</version>
+			<version>3.5.0</version>
 		</dependency>
 
 	</dependencies>