Merge remote-tracking branch 'origin/master' into 4634-rule-builder

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

@@ -0,0 +1,31 @@
+package ca.uhn.fhir.util;
+
+/**
+ * A utility class for thread sleeps.
+ * Uses non-static methods for easier mocking and unnecessary waits in unit tests
+ */
+public class SleepUtil {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SleepUtil.class);
+
+	public void sleepAtLeast(long theMillis) {
+		sleepAtLeast(theMillis, true);
+	}
+
+	@SuppressWarnings("BusyWait")
+	public void sleepAtLeast(long theMillis, boolean theLogProgress) {
+		long start = System.currentTimeMillis();
+		while (System.currentTimeMillis() <= start + theMillis) {
+			try {
+				long timeSinceStarted = System.currentTimeMillis() - start;
+				long timeToSleep = Math.max(0, theMillis - timeSinceStarted);
+				if (theLogProgress) {
+					ourLog.info("Sleeping for {}ms", timeToSleep);
+				}
+				Thread.sleep(timeToSleep);
+			} catch (InterruptedException e) {
+				Thread.currentThread().interrupt();
+				ourLog.error("Interrupted", e);
+			}
+		}
+	}
+}

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

@@ -31,6 +31,9 @@ import static org.apache.commons.lang3.StringUtils.defaultString;
 
 public class TestUtil {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TestUtil.class);
+
+	private static SleepUtil ourSleepUtil = new SleepUtil();
+
 	private static boolean ourShouldRandomizeTimezones = true;
 
 	public static void setShouldRandomizeTimezones(boolean theShouldRandomizeTimezones) {
@@ -135,25 +138,22 @@ public class TestUtil {
 		return stripReturns(theString).replace(" ", "");
 	}
 
+	/**
+	 *
+	 * In production code, instead of this static method, it is better to use an instance of SleepUtil.
+	 * Since SleepUtil isn't using static methods, it is easier to mock for unit test and avoid unnecessary waits in
+	 * unit tests
+	 */
 	public static void sleepAtLeast(long theMillis) {
-		sleepAtLeast(theMillis, true);
+		ourSleepUtil.sleepAtLeast(theMillis);
 	}
 
-	@SuppressWarnings("BusyWait")
+	/**
+	 * In production code, instead of this static method, it is better to use an instance of SleepUtil.
+	 * Since SleepUtil isn't using static methods, it is easier to mock for unit test and avoid unnecessary waits in
+	 * unit tests
+	 */
 	public static void sleepAtLeast(long theMillis, boolean theLogProgress) {
-		long start = System.currentTimeMillis();
+		ourSleepUtil.sleepAtLeast(theMillis, theLogProgress);
-		while (System.currentTimeMillis() <= start + theMillis) {
-			try {
-				long timeSinceStarted = System.currentTimeMillis() - start;
-				long timeToSleep = Math.max(0, theMillis - timeSinceStarted);
-				if (theLogProgress) {
-					ourLog.info("Sleeping for {}ms", timeToSleep);
-				}
-				Thread.sleep(timeToSleep);
-			} catch (InterruptedException e) {
-				Thread.currentThread().interrupt();
-				ourLog.error("Interrupted", e);
-			}
-		}
 	}
 }

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

@@ -0,0 +1,29 @@
+package ca.uhn.fhir.util;
+
+import org.junit.jupiter.api.Test;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+class SleepUtilTest {
+
+	@Test
+	public void testSleepAtLeast() {
+		SleepUtil sleepUtil = new SleepUtil();
+		long amountToSleepMs = 10;
+
+		long start = System.currentTimeMillis();
+		sleepUtil.sleepAtLeast(amountToSleepMs);
+		long stop = System.currentTimeMillis();
+
+		long actualSleepDurationMs = stop - start;
+		assertTrue(actualSleepDurationMs >= amountToSleepMs);
+	}
+
+	@Test
+	public void testZeroMs() {
+		// 0 is a valid input
+		SleepUtil sleepUtil = new SleepUtil();
+		sleepUtil.sleepAtLeast(0);
+	}
+
+}

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5553-deadlocks-on-mdm-clear.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 5553
+title: "mdm-clear jobs are prone to failing because of deadlocks when running on SQL Server. Such job failures have  
+been mitigated to some extent by increasing the retries on deadlocks."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5555-avoid-resource-lob-column.yaml

@@ -0,0 +1,10 @@
+---
+type: perf
+issue: 5555
+title: "Previously, resource body content went into one of 2 columns on the HFJ_RES_VER table: 
+    RES_TEXT if the size was above a configurable threshold, or RES_TEXT_VC if it was below that 
+    threshold. Performance testing has shown that the latter is always faster, and that on 
+    Postgres the use of the latter is particularly problematic since it maps to the
+    largeobject table which isn't the recommended way of storing high frequency objects. 
+    The configurable threshold is now ignored, and the latter column is always used. Any legacy
+    data in the former column will still be read however."

hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirH2Dialect.java

@@ -19,7 +19,6 @@
  */
 package ca.uhn.fhir.jpa.model.dialect;
 
-import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import org.hibernate.dialect.DatabaseVersion;
 import org.hibernate.dialect.H2Dialect;
 
@@ -38,7 +37,7 @@ public class HapiFhirH2Dialect extends H2Dialect {
 
 	/**
 	 * As of Hibernate 6, generated schemas include a column level check constraint that enforces valid values
-	 * for columns that back an Enum type. For example, the column definition for {@link ResourceTable#getFhirVersion()}
+	 * for columns that back an Enum type. For example, the column definition for <code>ResourceTable#getFhirVersion()</code>
 	 * would look like:
 	 * <pre>
 	 *  RES_VERSION varchar(7) check (RES_VERSION in ('DSTU2','DSTU2_HL7ORG','DSTU2_1','DSTU3','R4','R4B','R5')),

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

@@ -48,8 +48,10 @@ public final class HapiEntityManagerFactoryUtil {
 			ConfigurableListableBeanFactory myConfigurableListableBeanFactory,
 			FhirContext theFhirContext,
 			JpaStorageSettings theStorageSettings) {
+
 		LocalContainerEntityManagerFactoryBean retVal =
 				new HapiFhirLocalContainerEntityManagerFactoryBean(myConfigurableListableBeanFactory);
+
 		configureEntityManagerFactory(retVal, theFhirContext, theStorageSettings);
 		return retVal;
 	}

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

@@ -148,9 +148,7 @@ import org.springframework.transaction.support.TransactionSynchronization;
 import org.springframework.transaction.support.TransactionSynchronizationManager;
 import org.springframework.transaction.support.TransactionTemplate;
 
-import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.Date;
@@ -645,7 +643,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 			theEntity.setResourceType(toResourceName(theResource));
 		}
 
-		byte[] resourceBinary;
 		String resourceText;
 		ResourceEncodingEnum encoding;
 		boolean changed = false;
@@ -662,7 +659,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 				if (address != null) {
 
 					encoding = ResourceEncodingEnum.ESR;
-					resourceBinary = null;
 					resourceText = address.getProviderId() + ":" + address.getLocation();
 					changed = true;
 
@@ -680,19 +676,9 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 					theEntity.setFhirVersion(myContext.getVersion().getVersion());
 
 					HashFunction sha256 = Hashing.sha256();
-					HashCode hashCode;
+					resourceText = encodeResource(theResource, encoding, excludeElements, myContext);
-					String encodedResource = encodeResource(theResource, encoding, excludeElements, myContext);
+					encoding = ResourceEncodingEnum.JSON;
-					if (myStorageSettings.getInlineResourceTextBelowSize() > 0
+					HashCode hashCode = sha256.hashUnencodedChars(resourceText);
-							&& encodedResource.length() < myStorageSettings.getInlineResourceTextBelowSize()) {
-						resourceText = encodedResource;
-						resourceBinary = null;
-						encoding = ResourceEncodingEnum.JSON;
-						hashCode = sha256.hashUnencodedChars(encodedResource);
-					} else {
-						resourceText = null;
-						resourceBinary = getResourceBinary(encoding, encodedResource);
-						hashCode = sha256.hashBytes(resourceBinary);
-					}
 
 					String hashSha256 = hashCode.toString();
 					if (!hashSha256.equals(theEntity.getHashSha256())) {
@@ -710,7 +696,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 			} else {
 
 				encoding = null;
-				resourceBinary = null;
 				resourceText = null;
 			}
 
@@ -728,7 +713,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 				changed = true;
 			}
 
-			resourceBinary = null;
 			resourceText = null;
 			encoding = ResourceEncodingEnum.DEL;
 		}
@@ -753,46 +737,19 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 				if (currentHistoryVersion == null || !currentHistoryVersion.hasResource()) {
 					changed = true;
 				} else {
-					changed = !Arrays.equals(currentHistoryVersion.getResource(), resourceBinary);
+					changed = !StringUtils.equals(currentHistoryVersion.getResourceTextVc(), resourceText);
 				}
 			}
 		}
 
 		EncodedResource retVal = new EncodedResource();
 		retVal.setEncoding(encoding);
-		retVal.setResourceBinary(resourceBinary);
 		retVal.setResourceText(resourceText);
 		retVal.setChanged(changed);
 
 		return retVal;
 	}
 
-	/**
-	 * helper for returning the encoded byte array of the input resource string based on the encoding.
-	 *
-	 * @param encoding        the encoding to used
-	 * @param encodedResource the resource to encode
-	 * @return byte array of the resource
-	 */
-	@Nonnull
-	private byte[] getResourceBinary(ResourceEncodingEnum encoding, String encodedResource) {
-		byte[] resourceBinary;
-		switch (encoding) {
-			case JSON:
-				resourceBinary = encodedResource.getBytes(StandardCharsets.UTF_8);
-				break;
-			case JSONC:
-				resourceBinary = GZipUtil.compress(encodedResource);
-				break;
-			default:
-			case DEL:
-			case ESR:
-				resourceBinary = new byte[0];
-				break;
-		}
-		return resourceBinary;
-	}
-
 	/**
 	 * helper to format the meta element for serialization of the resource.
 	 *
@@ -1437,8 +1394,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 			List<String> excludeElements = new ArrayList<>(8);
 			getExcludedElements(historyEntity.getResourceType(), excludeElements, theResource.getMeta());
 			String encodedResourceString = encodeResource(theResource, encoding, excludeElements, myContext);
-			byte[] resourceBinary = getResourceBinary(encoding, encodedResourceString);
+			boolean changed = !StringUtils.equals(historyEntity.getResourceTextVc(), encodedResourceString);
-			boolean changed = !Arrays.equals(historyEntity.getResource(), resourceBinary);
 
 			historyEntity.setUpdated(theTransactionDetails.getTransactionDate());
 
@@ -1450,19 +1406,14 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 				return historyEntity;
 			}
 
-			if (getStorageSettings().getInlineResourceTextBelowSize() > 0
+			populateEncodedResource(encodedResource, encodedResourceString, ResourceEncodingEnum.JSON);
-					&& encodedResourceString.length() < getStorageSettings().getInlineResourceTextBelowSize()) {
-				populateEncodedResource(encodedResource, encodedResourceString, null, ResourceEncodingEnum.JSON);
-			} else {
-				populateEncodedResource(encodedResource, null, resourceBinary, encoding);
-			}
 		}
+
 		/*
 		 * Save the resource itself to the resourceHistoryTable
 		 */
 		historyEntity = myEntityManager.merge(historyEntity);
 		historyEntity.setEncoding(encodedResource.getEncoding());
-		historyEntity.setResource(encodedResource.getResourceBinary());
 		historyEntity.setResourceTextVc(encodedResource.getResourceText());
 		myResourceHistoryTableDao.save(historyEntity);
 
@@ -1472,12 +1423,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 	}
 
 	private void populateEncodedResource(
-			EncodedResource encodedResource,
+			EncodedResource encodedResource, String encodedResourceString, ResourceEncodingEnum theEncoding) {
-			String encodedResourceString,
-			byte[] theResourceBinary,
-			ResourceEncodingEnum theEncoding) {
 		encodedResource.setResourceText(encodedResourceString);
-		encodedResource.setResourceBinary(theResourceBinary);
 		encodedResource.setEncoding(theEncoding);
 	}
 
@@ -1542,7 +1489,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		}
 
 		historyEntry.setEncoding(theChanged.getEncoding());
-		historyEntry.setResource(theChanged.getResourceBinary());
 		historyEntry.setResourceTextVc(theChanged.getResourceText());
 
 		ourLog.debug("Saving history entry ID[{}] for RES_ID[{}]", historyEntry.getId(), historyEntry.getResourceId());

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

@@ -1689,19 +1689,17 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		if (historyEntity.getEncoding() == ResourceEncodingEnum.JSONC
 				|| historyEntity.getEncoding() == ResourceEncodingEnum.JSON) {
 			byte[] resourceBytes = historyEntity.getResource();
+
+			// Always migrate data out of the bytes column
 			if (resourceBytes != null) {
 				String resourceText = decodeResource(resourceBytes, historyEntity.getEncoding());
-				if (myStorageSettings.getInlineResourceTextBelowSize() > 0
+				ourLog.debug(
-						&& resourceText.length() < myStorageSettings.getInlineResourceTextBelowSize()) {
+						"Storing text of resource {} version {} as inline VARCHAR",
-					ourLog.debug(
+						entity.getResourceId(),
-							"Storing text of resource {} version {} as inline VARCHAR",
+						historyEntity.getVersion());
-							entity.getResourceId(),
+				historyEntity.setResourceTextVc(resourceText);
-							historyEntity.getVersion());
+				historyEntity.setEncoding(ResourceEncodingEnum.JSON);
-					historyEntity.setResourceTextVc(resourceText);
+				changed = true;
-					historyEntity.setResource(null);
-					historyEntity.setEncoding(ResourceEncodingEnum.JSON);
-					changed = true;
-				}
 			}
 		}
 		if (isBlank(historyEntity.getSourceUri()) && isBlank(historyEntity.getRequestId())) {
@@ -2071,6 +2069,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 				});
 	}
 
+	@Override
 	public <PID extends IResourcePersistentId<?>> Stream<PID> searchForIdStream(
 			SearchParameterMap theParams,
 			RequestDetails theRequest,

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

@@ -24,7 +24,6 @@ import ca.uhn.fhir.jpa.model.entity.ResourceEncodingEnum;
 class EncodedResource {
 
 	private boolean myChanged;
-	private byte[] myResource;
 	private ResourceEncodingEnum myEncoding;
 	private String myResourceText;
 
@@ -36,14 +35,6 @@ class EncodedResource {
 		myEncoding = theEncoding;
 	}
 
-	public byte[] getResourceBinary() {
-		return myResource;
-	}
-
-	public void setResourceBinary(byte[] theResource) {
-		myResource = theResource;
-	}
-
 	public boolean isChanged() {
 		return myChanged;
 	}

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

@@ -79,4 +79,16 @@ public interface IResourceHistoryTableDao extends JpaRepository<ResourceHistoryT
 	@Modifying
 	@Query("DELETE FROM ResourceHistoryTable t WHERE t.myId = :pid")
 	void deleteByPid(@Param("pid") Long theId);
+
+	/**
+	 * This method is only for use in unit tests - It is used to move the stored resource body contents from the new
+	 * <code>RES_TEXT_VC</code> column to the legacy <code>RES_TEXT</code> column, which is where data may have
+	 * been stored by versions of HAPI FHIR prior to 7.0.0
+	 *
+	 * @since 7.0.0
+	 */
+	@Modifying
+	@Query(
+			"UPDATE ResourceHistoryTable r SET r.myResourceTextVc = null, r.myResource = :text, r.myEncoding = 'JSONC' WHERE r.myId = :pid")
+	void updateNonInlinedContents(@Param("text") byte[] theText, @Param("pid") long thePid);
 }

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

@@ -1555,11 +1555,12 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 		Builder.BuilderWithTableName nrmlTable = version.onTable("HFJ_SPIDX_QUANTITY_NRML");
 		nrmlTable.addColumn("20210111.1", "PARTITION_ID").nullable().type(ColumnTypeEnum.INT);
 		nrmlTable.addColumn("20210111.2", "PARTITION_DATE").nullable().type(ColumnTypeEnum.DATE_ONLY);
-		// - The fk name is generated from Hibernate, have to use this name here
+		// Disabled - superceded by 20220304.33
 		nrmlTable
 				.addForeignKey("20210111.3", "FKRCJOVMUH5KC0O6FVBLE319PYV")
 				.toColumn("RES_ID")
-				.references("HFJ_RESOURCE", "RES_ID");
+				.references("HFJ_RESOURCE", "RES_ID")
+				.doNothing();
 
 		Builder.BuilderWithTableName quantityTable = version.onTable("HFJ_SPIDX_QUANTITY");
 		quantityTable

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/entity/GeneratedSchemaTest.java

@@ -0,0 +1,40 @@
+package ca.uhn.fhir.jpa.entity;
+
+import ca.uhn.fhir.util.ClasspathUtil;
+import org.apache.commons.lang3.StringUtils;
+import org.junit.jupiter.api.Test;
+
+import java.util.Arrays;
+
+import static org.hamcrest.CoreMatchers.containsString;
+import static org.hamcrest.MatcherAssert.assertThat;
+
+public class GeneratedSchemaTest {
+
+	/**
+	 * Make sure that the RES_TEXT_VC column, which is supposed to be an unlimited-length
+	 * string datatype, actually uses an appropriate datatype on the various databases
+	 * we care about.
+	 */
+	@Test
+	public void testVerifyLongVarcharColumnDefinition() {
+		validateLongVarcharDatatype("cockroachdb.sql", "varchar(2147483647)");
+		validateLongVarcharDatatype("derby.sql", "clob");
+		validateLongVarcharDatatype("mysql.sql", "longtext");
+		validateLongVarcharDatatype("mariadb.sql", "longtext");
+
+		validateLongVarcharDatatype("h2.sql", "clob");
+		validateLongVarcharDatatype("postgres.sql", "text");
+		validateLongVarcharDatatype("oracle.sql", "clob");
+		validateLongVarcharDatatype("sqlserver.sql", "varchar(max)");
+
+	}
+
+	private static void validateLongVarcharDatatype(String schemaName, String expectedDatatype) {
+		String schema = ClasspathUtil.loadResource("ca/uhn/hapi/fhir/jpa/docs/database/" + schemaName);
+		String[] lines = StringUtils.split(schema, '\n');
+		String resTextVc = Arrays.stream(lines).filter(t -> t.contains("RES_TEXT_VC ")).findFirst().orElseThrow();
+		assertThat("Wrong type in " + schemaName, resTextVc, containsString("RES_TEXT_VC " + expectedDatatype));
+	}
+
+}

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

@@ -25,14 +25,15 @@ import ca.uhn.fhir.rest.api.Constants;
 import jakarta.persistence.*;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
-import org.hibernate.annotations.JdbcTypeCode;
+import org.hibernate.Length;
 import org.hibernate.annotations.OptimisticLock;
-import org.hibernate.type.SqlTypes;
 
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Collection;
 
+import static org.apache.commons.lang3.StringUtils.defaultString;
+
 @Entity
 @Table(
 		name = ResourceHistoryTable.HFJ_RES_VER,
@@ -57,7 +58,6 @@ public class ResourceHistoryTable extends BaseHasResource implements Serializabl
 	public static final int ENCODING_COL_LENGTH = 5;
 
 	public static final String HFJ_RES_VER = "HFJ_RES_VER";
-	public static final int RES_TEXT_VC_MAX_LENGTH = 4000;
 	private static final long serialVersionUID = 1L;
 
 	@Id
@@ -86,13 +86,15 @@ public class ResourceHistoryTable extends BaseHasResource implements Serializabl
 	@OneToMany(mappedBy = "myResourceHistory", cascade = CascadeType.ALL, fetch = FetchType.LAZY, orphanRemoval = true)
 	private Collection<ResourceHistoryTag> myTags;
 
+	/**
+	 * Note: No setter for this field because it's only a legacy way of storing data now.
+	 */
 	@Column(name = "RES_TEXT", length = Integer.MAX_VALUE - 1, nullable = true)
 	@Lob()
 	@OptimisticLock(excluded = true)
 	private byte[] myResource;
 
-	@Column(name = "RES_TEXT_VC", length = RES_TEXT_VC_MAX_LENGTH, nullable = true)
+	@Column(name = "RES_TEXT_VC", nullable = true, length = Length.LONG32)
-	@JdbcTypeCode(SqlTypes.LONG32VARCHAR)
 	@OptimisticLock(excluded = true)
 	private String myResourceTextVc;
 
@@ -153,7 +155,8 @@ public class ResourceHistoryTable extends BaseHasResource implements Serializabl
 	}
 
 	public void setResourceTextVc(String theResourceTextVc) {
-		myResourceTextVc = theResourceTextVc;
+		myResource = null;
+		myResourceTextVc = defaultString(theResourceTextVc);
 	}
 
 	public ResourceHistoryProvenanceEntity getProvenance() {
@@ -209,10 +212,6 @@ public class ResourceHistoryTable extends BaseHasResource implements Serializabl
 		return myResource;
 	}
 
-	public void setResource(byte[] theResource) {
-		myResource = theResource;
-	}
-
 	@Override
 	public Long getResourceId() {
 		return myResourceId;

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/bulk/imprt2/ConsumeFilesStepR4Test.java

@@ -41,14 +41,12 @@ public class ConsumeFilesStepR4Test extends BasePartitioningR4Test {
 	public void before() throws Exception {
 		super.before();
 		myPartitionSettings.setPartitioningEnabled(false);
-		myStorageSettings.setInlineResourceTextBelowSize(10000);
 	}
 
 	@AfterEach
 	@Override
 	public void after() {
 		super.after();
-		myStorageSettings.setInlineResourceTextBelowSize(new JpaStorageSettings().getInlineResourceTextBelowSize());
 	}
 
 	@Test

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CreateTest.java

@@ -91,7 +91,6 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
 		myStorageSettings.setNormalizedQuantitySearchLevel(NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED);
 		myStorageSettings.setIndexOnContainedResources(new JpaStorageSettings().isIndexOnContainedResources());
 		myStorageSettings.setIndexOnContainedResourcesRecursively(new JpaStorageSettings().isIndexOnContainedResourcesRecursively());
-		myStorageSettings.setInlineResourceTextBelowSize(new JpaStorageSettings().getInlineResourceTextBelowSize());
 	}
 
 	@Test

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4InlineResourceModeTest.java

@@ -1,102 +1,61 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
-import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
+import ca.uhn.fhir.jpa.dao.GZipUtil;
-import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
+import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
+import ca.uhn.fhir.jpa.model.entity.ResourceEncodingEnum;
 import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
-import org.apache.commons.lang3.StringUtils;
+import ca.uhn.fhir.rest.param.DateRangeParam;
-import org.hl7.fhir.r4.model.IdType;
+import ca.uhn.fhir.rest.param.HistorySearchDateRangeParam;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Patient;
-import org.junit.jupiter.api.AfterEach;
-import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.util.HashMap;
 
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.containsString;
 import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
 public class FhirResourceDaoR4InlineResourceModeTest extends BaseJpaR4Test {
 
-	@BeforeEach
-	public void beforeSetDao() {
-		myStorageSettings.setInlineResourceTextBelowSize(5000);
-	}
-
-	@AfterEach
-	public void afterResetDao() {
-		myStorageSettings.setInlineResourceTextBelowSize(new JpaStorageSettings().getInlineResourceTextBelowSize());
-	}
-
 	@Test
-	public void testCreateWithInlineResourceTextStorage() {
+	public void testRetrieveNonInlinedResource() {
-		Patient patient = new Patient();
+		IIdType id = createPatient(withActiveTrue());
-		patient.setActive(true);
+		Long pid = id.getIdPartAsLong();
-		Long resourceId = myPatientDao.create(patient).getId().getIdPartAsLong();
 
-		patient = new Patient();
+		relocateResourceTextToCompressedColumn(pid, 1L);
-		patient.setId("Patient/" + resourceId);
-		patient.setActive(false);
-		myPatientDao.update(patient);
 
-		runInTransaction(() -> {
+		runInTransaction(()->{
-			// Version 1
+			ResourceHistoryTable historyEntity = myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(pid, 1);
-			ResourceHistoryTable entity = myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(resourceId, 1);
+			assertNotNull(historyEntity.getResource());
-			assertNull(entity.getResource());
+			assertNull(historyEntity.getResourceTextVc());
-			assertThat(entity.getResourceTextVc(), containsString("\"active\":true"));
+			assertEquals(ResourceEncodingEnum.JSONC, historyEntity.getEncoding());
-			// Version 2
-			entity = myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(resourceId, 2);
-			assertNull(entity.getResource());
-			assertThat(entity.getResourceTextVc(), containsString("\"active\":false"));
 		});
 
-		patient = myPatientDao.read(new IdType("Patient/" + resourceId));
+		// Read
-		assertFalse(patient.getActive());
+		validatePatient(myPatientDao.read(id.withVersion(null), mySrd));
 
-		patient = (Patient) myPatientDao.search(SearchParameterMap.newSynchronous()).getAllResources().get(0);
+		// VRead
-		assertFalse(patient.getActive());
+		validatePatient(myPatientDao.read(id.withVersion("1"), mySrd));
 
+		// Search (Sync)
+		validatePatient(myPatientDao.search(SearchParameterMap.newSynchronous(), mySrd).getResources(0, 1).get(0));
+
+		// Search (Async)
+		validatePatient(myPatientDao.search(new SearchParameterMap(), mySrd).getResources(0, 1).get(0));
+
+		// History
+		validatePatient(myPatientDao.history(id, new HistorySearchDateRangeParam(new HashMap<>(), new DateRangeParam(), 0), mySrd).getResources(0, 1).get(0));
 	}
 
 
-	@Test
+	private void validatePatient(IBaseResource theRead) {
-	public void testDontUseInlineAboveThreshold() {
+		assertTrue(((Patient)theRead).getActive());
-		String veryLongFamilyName = StringUtils.leftPad("", 6000, 'a');
-
-		Patient patient = new Patient();
-		patient.setActive(true);
-		patient.addName().setFamily(veryLongFamilyName);
-		Long resourceId = myPatientDao.create(patient).getId().getIdPartAsLong();
-
-		runInTransaction(() -> {
-			// Version 1
-			ResourceHistoryTable entity = myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(resourceId, 1);
-			assertNotNull(entity.getResource());
-			assertNull(entity.getResourceTextVc());
-		});
-
-		patient = myPatientDao.read(new IdType("Patient/" + resourceId));
-		assertEquals(veryLongFamilyName, patient.getNameFirstRep().getFamily());
-	}
-
-
-	@Test
-	public void testNopOnUnchangedUpdate() {
-		Patient patient = new Patient();
-		patient.setActive(true);
-		Long resourceId = myPatientDao.create(patient).getId().getIdPartAsLong();
-
-		patient = new Patient();
-		patient.setId("Patient/" + resourceId);
-		patient.setActive(true);
-		DaoMethodOutcome updateOutcome = myPatientDao.update(patient);
-		assertEquals("1", updateOutcome.getId().getVersionIdPart());
-		assertTrue(updateOutcome.isNop());
-
 	}
 
 

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4QueryCountTest.java

@@ -1031,26 +1031,15 @@ public class FhirResourceDaoR4QueryCountTest extends BaseResourceProviderR4Test
 
 	@ParameterizedTest
 	@CsvSource({
-		// NoOp    OptimisticLock  OptimizeMode      ExpectedSelect  ExpectedUpdate
+		// OptimisticLock  OptimizeMode      ExpectedSelect  ExpectedUpdate
-		"  false,  false,          CURRENT_VERSION,  2,              1",
+		"  false,          CURRENT_VERSION,  2,              0",
-		"  true,   false,          CURRENT_VERSION,  2,              0",
+		"  true,           CURRENT_VERSION,  12,             0",
-		"  false,  true,           CURRENT_VERSION,  12,             1",
+		"  false,          ALL_VERSIONS,     12,             0",
-		"  true,   true,           CURRENT_VERSION,  12,             0",
+		"  true,           ALL_VERSIONS,     22,             0",
-		"  false,  false,          ALL_VERSIONS,     12,             10",
-		"  true,   false,          ALL_VERSIONS,     12,             0",
-		"  false,  true,           ALL_VERSIONS,     22,             10",
-		"  true,   true,           ALL_VERSIONS,     22,             0",
 	})
-	public void testReindexJob_OptimizeStorage(boolean theNoOp, boolean theOptimisticLock, ReindexParameters.OptimizeStorageModeEnum theOptimizeStorageModeEnum, int theExpectedSelectCount, int theExpectedUpdateCount) {
+	public void testReindexJob_OptimizeStorage(boolean theOptimisticLock, ReindexParameters.OptimizeStorageModeEnum theOptimizeStorageModeEnum, int theExpectedSelectCount, int theExpectedUpdateCount) {
 		// Setup
 
-		// In no-op mode, the inlining is already in the state it needs to be in
-		if (theNoOp) {
-			myStorageSettings.setInlineResourceTextBelowSize(10000);
-		} else {
-			myStorageSettings.setInlineResourceTextBelowSize(0);
-		}
-
 		ResourceIdListWorkChunkJson data = new ResourceIdListWorkChunkJson();
 		IIdType patientId = createPatient(withActiveTrue());
 		for (int i = 0; i < 10; i++) {

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java

@@ -274,7 +274,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 			ResourceHistoryTable newHistory = table.toHistory(true);
 			ResourceHistoryTable currentHistory = myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(table.getId(), 1L);
 			newHistory.setEncoding(currentHistory.getEncoding());
-			newHistory.setResource(currentHistory.getResource());
+			newHistory.setResourceTextVc(currentHistory.getResourceTextVc());
 			myResourceHistoryTableDao.save(newHistory);
 		});
 
@@ -2928,7 +2928,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 				ResourceHistoryTable table = myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(id.getIdPartAsLong(), 1L);
 				String newContent = myFhirContext.newJsonParser().encodeResourceToString(p);
 				newContent = newContent.replace("male", "foo");
-				table.setResource(newContent.getBytes(Charsets.UTF_8));
+				table.setResourceTextVc(newContent);
 				table.setEncoding(ResourceEncodingEnum.JSON);
 				myResourceHistoryTableDao.save(table);
 			}

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4Test.java

@@ -620,11 +620,7 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
 		template.execute((TransactionCallback<ResourceTable>) t -> {
 			ResourceHistoryTable resourceHistoryTable = myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(id.getIdPartAsLong(), id.getVersionIdPartAsLong());
 			resourceHistoryTable.setEncoding(ResourceEncodingEnum.JSON);
-			try {
+			resourceHistoryTable.setResourceTextVc("{\"resourceType\":\"FOO\"}");
-				resourceHistoryTable.setResource("{\"resourceType\":\"FOO\"}".getBytes("UTF-8"));
-			} catch (UnsupportedEncodingException e) {
-				throw new Error(e);
-			}
 			myResourceHistoryTableDao.save(resourceHistoryTable);
 
 			ResourceTable table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalStateException::new);
@@ -1917,11 +1913,11 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
 
 		Patient p = new Patient();
 		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		myPatientDao.create(p, mySrd).getId();
+		myPatientDao.create(p, mySrd);
 
 		p = new Patient();
 		p.addIdentifier().setSystem("urn:system").setValue(methodName);
-		myPatientDao.create(p, mySrd).getId();
+		myPatientDao.create(p, mySrd);
 
 		Observation o = new Observation();
 		o.getCode().setText("Some Observation");

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

@@ -87,6 +87,11 @@ public class ReindexJobTest extends BaseJpaR4Test {
 			createPatient(withActiveTrue());
 		}
 
+		// Move resource text to compressed storage, which we don't write to anymore but legacy
+		// data may exist that was previously stored there, so we're simulating that.
+		List<ResourceHistoryTable> allHistoryEntities = runInTransaction(() -> myResourceHistoryTableDao.findAll());
+		allHistoryEntities.forEach(t->relocateResourceTextToCompressedColumn(t.getResourceId(), t.getVersion()));
+
 		runInTransaction(()->{
 			assertEquals(20, myResourceHistoryTableDao.count());
 			for (ResourceHistoryTable history : myResourceHistoryTableDao.findAll()) {
@@ -141,6 +146,11 @@ public class ReindexJobTest extends BaseJpaR4Test {
 			createPatient(withActiveTrue());
 		}
 
+		// Move resource text to compressed storage, which we don't write to anymore but legacy
+		// data may exist that was previously stored there, so we're simulating that.
+		List<ResourceHistoryTable> allHistoryEntities = runInTransaction(() -> myResourceHistoryTableDao.findAll());
+		allHistoryEntities.forEach(t->relocateResourceTextToCompressedColumn(t.getResourceId(), t.getVersion()));
+
 		runInTransaction(()->{
 			assertEquals(20, myResourceHistoryTableDao.count());
 			for (ResourceHistoryTable history : myResourceHistoryTableDao.findAll()) {
@@ -149,8 +159,6 @@ public class ReindexJobTest extends BaseJpaR4Test {
 			}
 		});
 
-		myStorageSettings.setInlineResourceTextBelowSize(10000);
-
 		// execute
 		JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
 		startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderInvalidDataR4Test.java

@@ -38,11 +38,9 @@ public class ResourceProviderInvalidDataR4Test extends BaseResourceProviderR4Tes
 		// Manually set the value to be an invalid decimal number
 		runInTransaction(() -> {
 			ResourceHistoryTable resVer = myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(id, 1);
-			byte[] bytesCompressed = resVer.getResource();
+			String resourceText = resVer.getResourceTextVc();
-			String resourceText = GZipUtil.decompress(bytesCompressed);
 			resourceText = resourceText.replace("100", "-.100");
-			bytesCompressed = GZipUtil.compress(resourceText);
+			resVer.setResourceTextVc(resourceText);
-			resVer.setResource(bytesCompressed);
 			myResourceHistoryTableDao.save(resVer);
 		});
 

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

@@ -54,6 +54,7 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
 import ca.uhn.fhir.util.ClasspathUtil;
 import ca.uhn.fhir.util.StopWatch;
+import ca.uhn.fhir.util.TestUtil;
 import ca.uhn.fhir.util.UrlUtil;
 import com.google.common.base.Charsets;
 import com.google.common.collect.Lists;
@@ -6723,7 +6724,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 		// Update Patient after delay
 		int delayInMs = 1000;
-		TimeUnit.MILLISECONDS.sleep(delayInMs);
+		TestUtil.sleepAtLeast(delayInMs + 100);
 		patient.getNameFirstRep().addGiven("Bob");
 		myClient.update().resource(patient).execute();
 

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/stresstest/GiantTransactionPerfTest.java

@@ -397,6 +397,11 @@ public class GiantTransactionPerfTest {
 			throw new UnsupportedOperationException();
 		}
 
+		@Override
+		public void updateNonInlinedContents(byte[] theText, long thePid) {
+			throw new UnsupportedOperationException();
+		}
+
 		@Nonnull
 		@Override
 		public List<ResourceHistoryTable> findAll() {

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

@@ -34,6 +34,20 @@
 			<scope>test</scope>
 		</dependency>
 
+		<!-- Needed for Testcontainers -->
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<version>4.13.2</version>
+			<scope>provided</scope>
+			<exclusions>
+				<exclusion>
+					<groupId>org.hamcrest</groupId>
+					<artifactId>hamcrest-core</artifactId>
+				</exclusion>
+			</exclusions>
+		</dependency>
+
 	</dependencies>
 
 	<build>

hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/database/BaseDatabaseVerificationIT.java

@@ -0,0 +1,148 @@
+package ca.uhn.fhir.jpa.dao.r5.database;
+
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.embedded.JpaEmbeddedDatabase;
+import ca.uhn.fhir.jpa.migrate.HapiMigrationStorageSvc;
+import ca.uhn.fhir.jpa.migrate.MigrationTaskList;
+import ca.uhn.fhir.jpa.migrate.SchemaMigrator;
+import ca.uhn.fhir.jpa.migrate.dao.HapiMigrationDao;
+import ca.uhn.fhir.jpa.migrate.tasks.HapiFhirJpaMigrationTasks;
+import ca.uhn.fhir.jpa.test.config.TestR5Config;
+import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
+import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
+import ca.uhn.fhir.util.VersionEnum;
+import jakarta.persistence.EntityManagerFactory;
+import org.apache.commons.lang3.StringUtils;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r5.model.Patient;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.ValueSource;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.data.envers.repository.support.EnversRevisionRepositoryFactoryBean;
+import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.junit.jupiter.SpringExtension;
+
+import javax.sql.DataSource;
+import java.util.Properties;
+import java.util.Set;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+
+@ExtendWith(SpringExtension.class)
+@EnableJpaRepositories(repositoryFactoryBeanClass = EnversRevisionRepositoryFactoryBean.class)
+@ContextConfiguration(classes = {BaseDatabaseVerificationIT.TestConfig.class})
+public abstract class BaseDatabaseVerificationIT {
+	private static final Logger ourLog = LoggerFactory.getLogger(BaseDatabaseVerificationIT.class);
+	private static final String MIGRATION_TABLENAME = "MIGRATIONS";
+
+	@Autowired
+	EntityManagerFactory myEntityManagerFactory;
+
+	@Autowired
+	JpaEmbeddedDatabase myJpaEmbeddedDatabase;
+
+	@Autowired
+	IFhirResourceDao<Patient> myPatientDao;
+
+
+	@ParameterizedTest
+	@ValueSource(ints = {10, 100000})
+	public void testCreateRead(int theSize) {
+		String name = StringUtils.leftPad("", theSize, "a");
+
+		Patient patient = new Patient();
+		patient.setActive(true);
+		patient.addName().setFamily(name);
+		IIdType id = myPatientDao.create(patient, new SystemRequestDetails()).getId();
+
+		Patient actual = myPatientDao.read(id, new SystemRequestDetails());
+		assertEquals(name, actual.getName().get(0).getFamily());
+	}
+
+
+	@Test
+	public void testDelete() {
+		Patient patient = new Patient();
+		patient.setActive(true);
+		IIdType id = myPatientDao.create(patient, new SystemRequestDetails()).getId().toUnqualifiedVersionless();
+
+		myPatientDao.delete(id, new SystemRequestDetails());
+
+		assertThrows(ResourceGoneException.class, () -> myPatientDao.read(id, new SystemRequestDetails()));
+	}
+
+
+	@Configuration
+	public static class TestConfig extends TestR5Config {
+
+		@Autowired
+		private JpaDatabaseContextConfigParamObject myJpaDatabaseContextConfigParamObject;
+
+		@Override
+		@Bean
+		public DataSource dataSource() {
+			DataSource dataSource = myJpaDatabaseContextConfigParamObject.getJpaEmbeddedDatabase().getDataSource();
+
+			HapiMigrationDao hapiMigrationDao = new HapiMigrationDao(dataSource, myJpaDatabaseContextConfigParamObject.getJpaEmbeddedDatabase().getDriverType(), MIGRATION_TABLENAME);
+			HapiMigrationStorageSvc hapiMigrationStorageSvc = new HapiMigrationStorageSvc(hapiMigrationDao);
+
+			MigrationTaskList tasks = new HapiFhirJpaMigrationTasks(Set.of()).getAllTasks(VersionEnum.values());
+
+			SchemaMigrator schemaMigrator = new SchemaMigrator(
+				"HAPI FHIR", MIGRATION_TABLENAME, dataSource, new Properties(), tasks, hapiMigrationStorageSvc);
+			schemaMigrator.setDriverType(myJpaDatabaseContextConfigParamObject.getJpaEmbeddedDatabase().getDriverType());
+
+			ourLog.info("About to run migration...");
+			schemaMigrator.createMigrationTableIfRequired();
+			schemaMigrator.migrate();
+			ourLog.info("Migration complete");
+
+
+			return dataSource;
+		}
+
+		@Bean
+		public JpaEmbeddedDatabase jpaEmbeddedDatabase(JpaDatabaseContextConfigParamObject theJpaDatabaseContextConfigParamObject) {
+			return theJpaDatabaseContextConfigParamObject.getJpaEmbeddedDatabase();
+		}
+
+		@Override
+		protected Properties jpaProperties() {
+			Properties retVal = super.jpaProperties();
+			retVal.put("hibernate.hbm2ddl.auto", "none");
+			retVal.put("hibernate.dialect", myJpaDatabaseContextConfigParamObject.getDialect());
+			return retVal;
+		}
+
+	}
+
+	public static class JpaDatabaseContextConfigParamObject {
+		private JpaEmbeddedDatabase myJpaEmbeddedDatabase;
+		private String myDialect;
+
+		public JpaDatabaseContextConfigParamObject(JpaEmbeddedDatabase theJpaEmbeddedDatabase, String theDialect) {
+			myJpaEmbeddedDatabase = theJpaEmbeddedDatabase;
+			myDialect = theDialect;
+		}
+
+		public JpaEmbeddedDatabase getJpaEmbeddedDatabase() {
+			return myJpaEmbeddedDatabase;
+		}
+
+		public String getDialect() {
+			return myDialect;
+		}
+	}
+
+
+}
+
+

hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/database/DatabaseVerificationWithMsSqlIT.java

@@ -0,0 +1,27 @@
+package ca.uhn.fhir.jpa.dao.r5.database;
+
+import ca.uhn.fhir.jpa.embedded.MsSqlEmbeddedDatabase;
+import ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect;
+import ca.uhn.fhir.jpa.model.dialect.HapiFhirSQLServerDialect;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.test.context.ContextConfiguration;
+
+@ContextConfiguration(classes = {
+	DatabaseVerificationWithMsSqlIT.TestConfig.class
+})
+public class DatabaseVerificationWithMsSqlIT extends BaseDatabaseVerificationIT {
+
+	@Configuration
+	public static class TestConfig {
+		@Bean
+		public JpaDatabaseContextConfigParamObject jpaDatabaseParamObject() {
+			return new JpaDatabaseContextConfigParamObject(
+				new MsSqlEmbeddedDatabase(),
+				HapiFhirSQLServerDialect.class.getName()
+			);
+		}
+	}
+
+
+}

hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/database/DatabaseVerificationWithOracleIT.java

@@ -0,0 +1,26 @@
+package ca.uhn.fhir.jpa.dao.r5.database;
+
+import ca.uhn.fhir.jpa.embedded.OracleEmbeddedDatabase;
+import ca.uhn.fhir.jpa.model.dialect.HapiFhirOracleDialect;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.test.context.ContextConfiguration;
+
+@ContextConfiguration(classes = {
+	DatabaseVerificationWithOracleIT.TestConfig.class
+})
+public class DatabaseVerificationWithOracleIT extends BaseDatabaseVerificationIT {
+
+	@Configuration
+	public static class TestConfig {
+		@Bean
+		public JpaDatabaseContextConfigParamObject jpaDatabaseParamObject(){
+			return new JpaDatabaseContextConfigParamObject(
+				new OracleEmbeddedDatabase(),
+				HapiFhirOracleDialect.class.getName()
+			);
+		}
+	}
+
+
+}

hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/database/DatabaseVerificationWithPostgresIT.java

@@ -0,0 +1,26 @@
+package ca.uhn.fhir.jpa.dao.r5.database;
+
+import ca.uhn.fhir.jpa.embedded.PostgresEmbeddedDatabase;
+import ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.test.context.ContextConfiguration;
+
+@ContextConfiguration(classes = {
+	DatabaseVerificationWithPostgresIT.TestConfig.class
+})
+public class DatabaseVerificationWithPostgresIT extends BaseDatabaseVerificationIT {
+
+	@Configuration
+	public static class TestConfig {
+		@Bean
+		public JpaDatabaseContextConfigParamObject jpaDatabaseParamObject() {
+			return new JpaDatabaseContextConfigParamObject(
+				new PostgresEmbeddedDatabase(),
+				HapiFhirPostgresDialect.class.getName()
+			);
+		}
+	}
+
+
+}

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

@@ -131,20 +131,14 @@
 		<dependency>
 			<groupId>org.testcontainers</groupId>
 			<artifactId>postgresql</artifactId>
-			<version>1.17.6</version>
-			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.testcontainers</groupId>
 			<artifactId>mssqlserver</artifactId>
-			<version>1.17.6</version>
-			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.testcontainers</groupId>
 			<artifactId>oracle-xe</artifactId>
-			<version>1.17.6</version>
-			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.postgresql</groupId>

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

@@ -20,6 +20,7 @@
 package ca.uhn.fhir.jpa.embedded;
 
 import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
+import jakarta.annotation.PreDestroy;
 import org.apache.commons.lang3.StringUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -53,6 +54,7 @@ public abstract class JpaEmbeddedDatabase {
 	private JdbcTemplate myJdbcTemplate;
 	private Connection myConnection;
 
+	@PreDestroy
 	public abstract void stop();
 
 	public abstract void disableConstraints();
@@ -116,7 +118,7 @@ public abstract class JpaEmbeddedDatabase {
 			for (String sql : theStatements) {
 				if (!StringUtils.isBlank(sql)) {
 					statement.addBatch(sql);
-					ourLog.info("Added to batch: {}", sql);
+					ourLog.debug("Added to batch: {}", sql);
 				}
 			}
 			statement.executeBatch();

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

@@ -40,6 +40,7 @@ import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
 import ca.uhn.fhir.jpa.binary.interceptor.BinaryStorageInterceptor;
 import ca.uhn.fhir.jpa.binary.provider.BinaryAccessProvider;
 import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportJobSchedulingHelper;
+import ca.uhn.fhir.jpa.dao.GZipUtil;
 import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
 import ca.uhn.fhir.jpa.dao.data.IBatch2JobInstanceRepository;
 import ca.uhn.fhir.jpa.dao.data.IBatch2WorkChunkRepository;
@@ -82,6 +83,7 @@ import ca.uhn.fhir.jpa.entity.TermValueSet;
 import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
 import ca.uhn.fhir.jpa.interceptor.PerformanceTracingLoggingInterceptor;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
+import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
 import ca.uhn.fhir.jpa.packages.IPackageInstallerSvc;
 import ca.uhn.fhir.jpa.partition.IPartitionLookupSvc;
 import ca.uhn.fhir.jpa.provider.JpaSystemProvider;
@@ -663,6 +665,14 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
 		return myTxManager;
 	}
 
+	protected void relocateResourceTextToCompressedColumn(Long theResourcePid, Long theVersion) {
+		runInTransaction(()->{
+			ResourceHistoryTable historyEntity = myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(theResourcePid, theVersion);
+			byte[] contents = GZipUtil.compress(historyEntity.getResourceTextVc());
+			myResourceHistoryTableDao.updateNonInlinedContents(contents, historyEntity.getId());
+		});
+	}
+
 	protected ValidationResult validateWithResult(IBaseResource theResource) {
 		FhirValidator validatorModule = myFhirContext.newValidator();
 		FhirInstanceValidator instanceValidator = new FhirInstanceValidator(myValidationSupport);

hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/config/TestR5Config.java

@@ -186,7 +186,7 @@ public class TestR5Config {
 		return retVal;
 	}
 
-	private Properties jpaProperties() {
+	protected Properties jpaProperties() {
 		Properties extraProperties = new Properties();
 		extraProperties.put("hibernate.format_sql", "false");
 		extraProperties.put("hibernate.show_sql", "false");

hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/ColumnTypeEnum.java

@@ -34,7 +34,7 @@ public enum ColumnTypeEnum {
 
 	/**
 	 * Unlimited length text, with a column definition containing the annotation:
-	 * <code>@JdbcTypeCode(SqlTypes.LONG32VARCHAR)</code>
+	 * <code>@Column(length=Integer.MAX_VALUE)</code>
 	 */
 	TEXT,
 	BIG_DECIMAL;

hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/ColumnTypeToDriverTypeToSqlType.java

@@ -62,7 +62,7 @@ public final class ColumnTypeToDriverTypeToSqlType {
 		setColumnType(ColumnTypeEnum.DOUBLE, DriverTypeEnum.MYSQL_5_7, "double precision");
 		setColumnType(ColumnTypeEnum.DOUBLE, DriverTypeEnum.MSSQL_2012, "double precision");
 		setColumnType(ColumnTypeEnum.DOUBLE, DriverTypeEnum.ORACLE_12C, "double precision");
-		setColumnType(ColumnTypeEnum.DOUBLE, DriverTypeEnum.POSTGRES_9_4, "float8");
+		setColumnType(ColumnTypeEnum.DOUBLE, DriverTypeEnum.POSTGRES_9_4, "double precision");
 
 		setColumnType(ColumnTypeEnum.LONG, DriverTypeEnum.H2_EMBEDDED, "bigint");
 		setColumnType(ColumnTypeEnum.LONG, DriverTypeEnum.DERBY_EMBEDDED, "bigint");
@@ -123,7 +123,7 @@ public final class ColumnTypeToDriverTypeToSqlType {
 				"oid"); // the PG driver will write oid into a `text` column
 		setColumnType(ColumnTypeEnum.CLOB, DriverTypeEnum.MSSQL_2012, "varchar(MAX)");
 
-		setColumnType(ColumnTypeEnum.TEXT, DriverTypeEnum.H2_EMBEDDED, "character large object");
+		setColumnType(ColumnTypeEnum.TEXT, DriverTypeEnum.H2_EMBEDDED, "clob");
 		setColumnType(ColumnTypeEnum.TEXT, DriverTypeEnum.DERBY_EMBEDDED, "clob");
 		setColumnType(ColumnTypeEnum.TEXT, DriverTypeEnum.MARIADB_10_1, "longtext");
 		setColumnType(ColumnTypeEnum.TEXT, DriverTypeEnum.MYSQL_5_7, "longtext");

hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/api/config/JpaStorageSettings.java

@@ -267,14 +267,6 @@ public class JpaStorageSettings extends StorageSettings {
 	 * @since 5.6.0
 	 */
 	private boolean myAdvancedHSearchIndexing = false;
-	/**
-	 * If set to a positive number, any resources with a character length at or below the given number
-	 * of characters will be stored inline in the <code>HFJ_RES_VER</code> table instead of using a
-	 * separate LOB column.
-	 *
-	 * @since 5.7.0
-	 */
-	private int myInlineResourceTextBelowSize = 0;
 
 	/**
 	 * @since 5.7.0
@@ -381,25 +373,21 @@ public class JpaStorageSettings extends StorageSettings {
 	}
 
 	/**
-	 * If set to a positive number, any resources with a character length at or below the given number
-	 * of characters will be stored inline in the <code>HFJ_RES_VER</code> table instead of using a
-	 * separate LOB column.
-	 *
 	 * @since 5.7.0
+	 * @deprecated This setting no longer does anything as of HAPI FHIR 7.0.0
 	 */
+	@Deprecated
 	public int getInlineResourceTextBelowSize() {
-		return myInlineResourceTextBelowSize;
+		return 0;
 	}
 
 	/**
-	 * If set to a positive number, any resources with a character length at or below the given number
-	 * of characters will be stored inline in the <code>HFJ_RES_VER</code> table instead of using a
-	 * separate LOB column.
-	 *
 	 * @since 5.7.0
+	 * @deprecated This setting no longer does anything as of HAPI FHIR 7.0.0
 	 */
+	@Deprecated
 	public void setInlineResourceTextBelowSize(int theInlineResourceTextBelowSize) {
-		myInlineResourceTextBelowSize = theInlineResourceTextBelowSize;
+		// ignored
 	}
 
 	/**

hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/tx/HapiTransactionService.java

@@ -36,7 +36,7 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
 import ca.uhn.fhir.util.ICallable;
-import ca.uhn.fhir.util.TestUtil;
+import ca.uhn.fhir.util.SleepUtil;
 import com.google.common.annotations.VisibleForTesting;
 import jakarta.annotation.Nonnull;
 import jakarta.annotation.Nullable;
@@ -48,6 +48,7 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.dao.DataIntegrityViolationException;
+import org.springframework.dao.PessimisticLockingFailureException;
 import org.springframework.orm.ObjectOptimisticLockingFailureException;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.TransactionStatus;
@@ -89,11 +90,18 @@ public class HapiTransactionService implements IHapiTransactionService {
 
 	private Propagation myTransactionPropagationWhenChangingPartitions = Propagation.REQUIRED;
 
+	private SleepUtil mySleepUtil = new SleepUtil();
+
 	@VisibleForTesting
 	public void setInterceptorBroadcaster(IInterceptorBroadcaster theInterceptorBroadcaster) {
 		myInterceptorBroadcaster = theInterceptorBroadcaster;
 	}
 
+	@VisibleForTesting
+	public void setSleepUtil(SleepUtil theSleepUtil) {
+		mySleepUtil = theSleepUtil;
+	}
+
 	@Override
 	public IExecutionBuilder withRequest(@Nullable RequestDetails theRequestDetails) {
 		return new ExecutionBuilder(theRequestDetails);
@@ -281,6 +289,25 @@ public class HapiTransactionService implements IHapiTransactionService {
 		return doExecuteInTransaction(theExecutionBuilder, theCallback, requestPartitionId, previousRequestPartitionId);
 	}
 
+	private boolean isThrowableOrItsSubclassPresent(Throwable theThrowable, Class<? extends Throwable> theClass) {
+		return ExceptionUtils.indexOfType(theThrowable, theClass) != -1;
+	}
+
+	private boolean isThrowablePresent(Throwable theThrowable, Class<? extends Throwable> theClass) {
+		return ExceptionUtils.indexOfThrowable(theThrowable, theClass) != -1;
+	}
+
+	private boolean isRetriable(Throwable theThrowable) {
+		return isThrowablePresent(theThrowable, ResourceVersionConflictException.class)
+				|| isThrowablePresent(theThrowable, DataIntegrityViolationException.class)
+				|| isThrowablePresent(theThrowable, ConstraintViolationException.class)
+				|| isThrowablePresent(theThrowable, ObjectOptimisticLockingFailureException.class)
+				// calling isThrowableOrItsSubclassPresent instead of isThrowablePresent for
+				// PessimisticLockingFailureException, because we want to retry on its subclasses as well,  especially
+				// CannotAcquireLockException, which is thrown in some deadlock situations which we want to retry
+				|| isThrowableOrItsSubclassPresent(theThrowable, PessimisticLockingFailureException.class);
+	}
+
 	@Nullable
 	private <T> T doExecuteInTransaction(
 			ExecutionBuilder theExecutionBuilder,
@@ -294,11 +321,7 @@ public class HapiTransactionService implements IHapiTransactionService {
 					return doExecuteCallback(theExecutionBuilder, theCallback);
 
 				} catch (Exception e) {
-					if (!(ExceptionUtils.indexOfThrowable(e, ResourceVersionConflictException.class) != -1
+					if (!isRetriable(e)) {
-							|| ExceptionUtils.indexOfThrowable(e, DataIntegrityViolationException.class) != -1
-							|| ExceptionUtils.indexOfThrowable(e, ConstraintViolationException.class) != -1
-							|| ExceptionUtils.indexOfThrowable(e, ObjectOptimisticLockingFailureException.class)
-									!= -1)) {
 						ourLog.debug("Unexpected transaction exception. Will not be retried.", e);
 						throw e;
 					} else {
@@ -354,7 +377,7 @@ public class HapiTransactionService implements IHapiTransactionService {
 							}
 							double sleepAmount = (250.0d * i) * Math.random();
 							long sleepAmountLong = (long) sleepAmount;
-							TestUtil.sleepAtLeast(sleepAmountLong, false);
+							mySleepUtil.sleepAtLeast(sleepAmountLong, false);
 
 							ourLog.info(
 									"About to start a transaction retry due to conflict or constraint error. Sleeping {}ms first.",

hapi-fhir-storage/src/test/java/ca/uhn/fhir/jpa/dao/tx/HapiTransactionServiceTest.java

@@ -0,0 +1,194 @@
+package ca.uhn.fhir.jpa.dao.tx;
+
+import ca.uhn.fhir.interceptor.api.HookParams;
+import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
+import ca.uhn.fhir.interceptor.api.Pointcut;
+import ca.uhn.fhir.jpa.api.model.ResourceVersionConflictResolutionStrategy;
+import ca.uhn.fhir.jpa.model.config.PartitionSettings;
+import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
+import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
+import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
+import ca.uhn.fhir.util.SleepUtil;
+import org.hibernate.exception.ConstraintViolationException;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.MethodSource;
+import org.mockito.Mock;
+import org.mockito.junit.jupiter.MockitoExtension;
+import org.springframework.dao.CannotAcquireLockException;
+import org.springframework.dao.DataIntegrityViolationException;
+import org.springframework.orm.ObjectOptimisticLockingFailureException;
+import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.TransactionStatus;
+import org.springframework.transaction.support.TransactionCallback;
+
+import java.sql.SQLException;
+import java.util.concurrent.atomic.AtomicInteger;
+import java.util.stream.Stream;
+
+import static org.junit.jupiter.api.Assertions.*;
+import static org.junit.jupiter.params.provider.Arguments.arguments;
+import static org.mockito.ArgumentMatchers.anyBoolean;
+import static org.mockito.ArgumentMatchers.anyLong;
+import static org.mockito.ArgumentMatchers.eq;
+import static org.mockito.ArgumentMatchers.isA;
+import static org.mockito.Mockito.lenient;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
+import static org.mockito.Mockito.verifyNoInteractions;
+import static org.mockito.Mockito.when;
+
+@ExtendWith(MockitoExtension.class)
+class HapiTransactionServiceTest {
+
+	@Mock
+	private IInterceptorBroadcaster myInterceptorBroadcasterMock;
+
+	@Mock
+	private PlatformTransactionManager myTransactionManagerMock;
+
+	@Mock
+	private IRequestPartitionHelperSvc myRequestPartitionHelperSvcMock;
+	@Mock
+	private PartitionSettings myPartitionSettingsMock;
+
+	@Mock
+	private SleepUtil mySleepUtilMock;
+
+	private HapiTransactionService myHapiTransactionService;
+
+
+	@BeforeEach
+	public void beforeEach() {
+		myHapiTransactionService = new HapiTransactionService();
+		myHapiTransactionService.setTransactionManager(myTransactionManagerMock);
+		myHapiTransactionService.setInterceptorBroadcaster(myInterceptorBroadcasterMock);
+		myHapiTransactionService.setPartitionSettingsForUnitTest(myPartitionSettingsMock);
+		myHapiTransactionService.setRequestPartitionSvcForUnitTest(myRequestPartitionHelperSvcMock);
+		myHapiTransactionService.setSleepUtil(mySleepUtilMock);
+		mockInterceptorBroadcaster();
+	}
+
+	private void mockInterceptorBroadcaster() {
+		lenient().when(myInterceptorBroadcasterMock.callHooksAndReturnObject(eq(Pointcut.STORAGE_VERSION_CONFLICT),
+			isA(HookParams.class)))
+			.thenAnswer(invocationOnMock -> {
+				HookParams hookParams = (HookParams) invocationOnMock.getArguments()[1];
+				//answer with whatever retry settings passed in as HookParam
+				RequestDetails requestDetails = hookParams.get(RequestDetails.class);
+				ResourceVersionConflictResolutionStrategy answer = new ResourceVersionConflictResolutionStrategy();
+				answer.setRetry(requestDetails.isRetry());
+				answer.setMaxRetries(requestDetails.getMaxRetries());
+				return answer;
+			});
+	}
+
+
+	/**
+	 * A helper method to test retry logic on exceptions
+	 * TransactionCallback interface allows only throwing RuntimeExceptions,
+	 * that's why the parameter type is RunTimeException
+	 */
+	private Exception testRetriesOnException(RuntimeException theException,
+											 boolean theRetryEnabled,
+											 int theMaxRetries,
+											 int theExpectedNumberOfCallsToTransactionCallback) {
+		RequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setRetry(theRetryEnabled);
+		requestDetails.setMaxRetries(theMaxRetries);
+
+		HapiTransactionService.IExecutionBuilder executionBuilder = myHapiTransactionService
+			.withRequest(requestDetails)
+			.withTransactionDetails(new TransactionDetails());
+
+		AtomicInteger numberOfCalls = new AtomicInteger();
+		TransactionCallback<Void> transactionCallback = (TransactionStatus theStatus) -> {
+			numberOfCalls.incrementAndGet();
+			throw theException;
+		};
+
+		Exception theExceptionThrownByDoExecute = assertThrows(Exception.class, () -> {
+			myHapiTransactionService.doExecute((HapiTransactionService.ExecutionBuilder) executionBuilder, transactionCallback);
+		});
+
+		assertEquals(theExpectedNumberOfCallsToTransactionCallback, numberOfCalls.get());
+		verify(mySleepUtilMock, times(theExpectedNumberOfCallsToTransactionCallback - 1))
+			.sleepAtLeast(anyLong(), anyBoolean());
+		return theExceptionThrownByDoExecute;
+	}
+
+	private static Stream<Arguments> provideRetriableExceptionParameters() {
+		String exceptionMessage = "failed!";
+		return Stream.of(
+			arguments(new ResourceVersionConflictException(exceptionMessage)),
+			arguments(new DataIntegrityViolationException(exceptionMessage)),
+			arguments(new ConstraintViolationException(exceptionMessage, new SQLException(""), null)),
+			arguments(new ObjectOptimisticLockingFailureException(exceptionMessage, new Exception())),
+			//CannotAcquireLockException is a subclass of
+			//PessimisticLockingFailureException which we treat as a retriable exception
+			arguments(new CannotAcquireLockException(exceptionMessage))
+		);
+	}
+
+	@ParameterizedTest(name = "{index}: {0}")
+	@MethodSource(value = "provideRetriableExceptionParameters")
+	void testDoExecute_WhenRetryEnabled_RetriesOnRetriableExceptions(RuntimeException theException) {
+		testRetriesOnException(theException, true, 2, 3);
+	}
+
+
+	@ParameterizedTest(name = "{index}: {0}")
+	@MethodSource(value = "provideRetriableExceptionParameters")
+	void testDoExecute_WhenRetryEnabled_RetriesOnRetriableInnerExceptions(RuntimeException theException) {
+		//in this test we wrap the retriable exception to test that nested exceptions are covered as well
+		RuntimeException theWrapperException = new RuntimeException("this is the wrapper", theException);
+		testRetriesOnException(theWrapperException, true, 2, 3);
+	}
+
+	@ParameterizedTest(name = "{index}: {0}")
+	@MethodSource(value = "provideRetriableExceptionParameters")
+	void testDoExecute_WhenRetryIsDisabled_DoesNotRetryExceptions(RuntimeException theException) {
+		testRetriesOnException(theException, false, 10, 1);
+	}
+
+	@Test
+	void testDoExecute_WhenRetryEnabled_DoesNotRetryOnNonRetriableException() {
+		RuntimeException nonRetriableException = new RuntimeException("should not be retried");
+		Exception exceptionThrown = testRetriesOnException(nonRetriableException, true, 10, 1);
+		assertEquals(nonRetriableException, exceptionThrown);
+		verifyNoInteractions(myInterceptorBroadcasterMock);
+	}
+
+	@Test
+	void testDoExecute_WhenRetyEnabled_StopsRetryingWhenARetryIsSuccessfull() {
+		RequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setRetry(true);
+		requestDetails.setMaxRetries(10);
+
+		HapiTransactionService.IExecutionBuilder executionBuilder = myHapiTransactionService
+			.withRequest(requestDetails)
+			.withTransactionDetails(new TransactionDetails());
+
+		AtomicInteger numberOfCalls = new AtomicInteger();
+		TransactionCallback<Void> transactionCallback = (TransactionStatus theStatus) -> {
+			int currentCallNum = numberOfCalls.incrementAndGet();
+			//fail for the first two calls then succeed on the third
+			if (currentCallNum < 3) {
+				// using ResourceVersionConflictException, since it is a retriable exception
+				throw new ResourceVersionConflictException("failed");
+			}
+			return null;
+		};
+
+		myHapiTransactionService.doExecute((HapiTransactionService.ExecutionBuilder) executionBuilder, transactionCallback);
+
+		assertEquals(3, numberOfCalls.get());
+		verify(mySleepUtilMock, times(2))
+			.sleepAtLeast(anyLong(), anyBoolean());
+	}
+}

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

@@ -361,9 +361,6 @@ public class JpaModelScannerAndVerifier {
 					if (!theIsView && column.length() == 255) {
 						throw new IllegalStateException(Msg.code(1626) + "Field does not have an explicit maximum length specified: " + field);
 					}
-					if (column.length() > MAX_COL_LENGTH) {
-						throw new IllegalStateException(Msg.code(1627) + "Field is too long: " + field);
-					}
 				}
 
 				Size size = theAnnotatedElement.getAnnotation(Size.class);

hapi-tinder-plugin/pom.xml

@@ -184,14 +184,6 @@
 		<dependency>
 			<groupId>org.apache.maven</groupId>
 			<artifactId>maven-plugin-api</artifactId>
-			<!--
-            <exclusions>
-				<exclusion>
-					<groupId>org.eclipse.sisu</groupId>
-					<artifactId>org.eclipse.sisu.plexus</artifactId>
-				</exclusion>
-			</exclusions>
-			-->
 		</dependency>
 		<dependency>
 			<groupId>org.apache.maven.plugin-tools</groupId>

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/ddl/DdlGeneratorHibernate61.java

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.tinder.ddl;
 
 import ca.uhn.fhir.jpa.util.ISequenceValueMassager;
+import ca.uhn.fhir.util.IoUtil;
 import jakarta.annotation.Nonnull;
 import jakarta.persistence.Entity;
 import jakarta.persistence.MappedSuperclass;
@@ -29,6 +30,7 @@ import org.springframework.core.io.ResourceLoader;
 import org.springframework.core.io.support.PathMatchingResourcePatternResolver;
 import org.springframework.core.type.filter.AnnotationTypeFilter;
 
+import java.io.Closeable;
 import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
@@ -125,19 +127,8 @@ public class DdlGeneratorHibernate61 {
 
 			writeContentsToFile(nextDialect.getAppendFile(), classLoader, outputFile);
 		}
-	}
 
-	private static void writeContentsToFile(String prependFile, ClassLoader classLoader, File outputFile)
+		IoUtil.closeQuietly(connectionProvider);
-			throws MojoFailureException {
-		if (isNotBlank(prependFile)) {
-			ResourceLoader loader = new DefaultResourceLoader(classLoader);
-			Resource resource = loader.getResource(prependFile);
-			try (Writer w = new FileWriter(outputFile, true)) {
-				w.append(resource.getContentAsString(StandardCharsets.UTF_8));
-			} catch (IOException e) {
-				throw new MojoFailureException("Failed to write to file " + outputFile + ": " + e.getMessage(), e);
-			}
-		}
 	}
 
 	public void setProject(MavenProject theProject) {
@@ -204,18 +195,64 @@ public class DdlGeneratorHibernate61 {
 	 * here. The schema export doesn't actually touch this DB, so it doesn't
 	 * matter that it doesn't correlate to the specified dialect.
 	 */
-	private static class FakeConnectionConnectionProvider extends UserSuppliedConnectionProviderImpl {
+	private static class FakeConnectionConnectionProvider extends UserSuppliedConnectionProviderImpl
+			implements Closeable {
 		private static final long serialVersionUID = 4147495169899817244L;
+		private Connection connection;
 
-		@Override
+		public FakeConnectionConnectionProvider() {
-		public Connection getConnection() throws SQLException {
+			try {
-			ourLog.trace("Using internal driver: {}", org.h2.Driver.class);
+				connection = DriverManager.getConnection("jdbc:h2:mem:tmp", "sa", "sa");
-			return DriverManager.getConnection("jdbc:h2:mem:tmp", "sa", "sa");
+			} catch (SQLException e) {
+				connection = null;
+				return;
+			}
+
+			/*
+			 * The Oracle Dialect tries to query for any existing sequences, so we need to supply
+			 * a fake empty table to answer that query.
+			 */
+			try {
+				connection.setAutoCommit(true);
+				connection
+						.prepareStatement("create table all_sequences (PID bigint not null, primary key (PID))")
+						.execute();
+			} catch (SQLException e) {
+				ourLog.error("Failed to create sequences table", e);
+			}
 		}
 
 		@Override
-		public void closeConnection(Connection conn) throws SQLException {
+		public Connection getConnection() {
-			conn.close();
+			ourLog.trace("Using internal driver: {}", org.h2.Driver.class);
+			return connection;
+		}
+
+		@Override
+		public void closeConnection(Connection conn) {
+			// ignore
+		}
+
+		@Override
+		public void close() throws IOException {
+			try {
+				connection.close();
+			} catch (SQLException e) {
+				throw new IOException(e);
+			}
+		}
+	}
+
+	private static void writeContentsToFile(String prependFile, ClassLoader classLoader, File outputFile)
+			throws MojoFailureException {
+		if (isNotBlank(prependFile)) {
+			ResourceLoader loader = new DefaultResourceLoader(classLoader);
+			Resource resource = loader.getResource(prependFile);
+			try (Writer w = new FileWriter(outputFile, true)) {
+				w.append(resource.getContentAsString(StandardCharsets.UTF_8));
+			} catch (IOException e) {
+				throw new MojoFailureException("Failed to write to file " + outputFile + ": " + e.getMessage(), e);
+			}
 		}
 	}
 }

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/ddl/GenerateDdlMojo.java

@@ -28,13 +28,13 @@ public class GenerateDdlMojo extends AbstractMojo {
 	private static final Logger ourLog = LoggerFactory.getLogger(GenerateDdlMojo.class);
 
 	@Parameter
-	private List<String> packageNames;
+	List<String> packageNames;
 
 	@Parameter
-	private List<Dialect> dialects;
+	List<Dialect> dialects;
 
 	@Parameter
-	private String outputDirectory;
+	String outputDirectory;
 
 	@Parameter(defaultValue = "${project}", readonly = true)
 	private transient MavenProject project;
@@ -70,18 +70,20 @@ public class GenerateDdlMojo extends AbstractMojo {
 
 	public static void main(String[] args) throws MojoExecutionException, MojoFailureException {
 		/*
-		 * Note, to execute this, add the following snippet to this module's POM. The whole project won't work with
+		 * Note, to execute this for real entities, add the following snippet to this module's POM. The whole project won't work with
 		 * that added, but you can add it temporarily in order to debug this in IJ:
 		 * 		<dependency>
 		 * 			<groupId>ca.uhn.hapi.fhir</groupId>
 		 * 			<artifactId>hapi-fhir-jpaserver-model</artifactId>
 		 * 			<version>${project.version}</version>
 		 * 		</dependency>
+		 *
+		 * Alternately, there is a unit test with fake entities that also runs this class.
 		 */
 		GenerateDdlMojo m = new GenerateDdlMojo();
 		m.packageNames = List.of("ca.uhn.fhir.jpa.model.entity");
 		m.outputDirectory = "hapi-tinder-plugin/target";
-		m.dialects = List.of(new Dialect("ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect", "h2.sql"));
+		m.dialects = List.of(new Dialect("ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect", "postgres.sql"));
 		m.execute();
 	}
 

hapi-tinder-plugin/src/test/java/ca/uhn/fhir/tinder/ddl/GenerateDdlMojoTest.java

@@ -0,0 +1,46 @@
+package ca.uhn.fhir.tinder.ddl;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.maven.plugin.MojoExecutionException;
+import org.apache.maven.plugin.MojoFailureException;
+import org.junit.jupiter.api.Test;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.util.List;
+import java.util.Locale;
+
+import static org.hamcrest.CoreMatchers.containsString;
+import static org.hamcrest.MatcherAssert.assertThat;
+
+class GenerateDdlMojoTest {
+
+	@Test
+	public void testGenerateSequences() throws MojoExecutionException, MojoFailureException, IOException {
+
+		GenerateDdlMojo m = new GenerateDdlMojo();
+		m.packageNames = List.of("ca.uhn.fhir.tinder.ddl.test");
+		m.outputDirectory = "target/generate-ddl-plugin-test/";
+		m.dialects = List.of(
+			new GenerateDdlMojo.Dialect("ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect", "h2.sql"),
+			new GenerateDdlMojo.Dialect("ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect", "postgres.sql"),
+			new GenerateDdlMojo.Dialect("ca.uhn.fhir.jpa.model.dialect.HapiFhirOracleDialect", "oracle.sql"),
+			new GenerateDdlMojo.Dialect("ca.uhn.fhir.jpa.model.dialect.HapiFhirSQLServerDialect", "sqlserver.sql")
+		);
+		m.execute();
+
+		verifySequence("sqlserver.sql");
+		verifySequence("oracle.sql");
+		verifySequence("postgres.sql");
+		verifySequence("h2.sql");
+
+	}
+
+	private static void verifySequence(String fileName) throws IOException {
+		String contents = FileUtils.readFileToString(new File("target/generate-ddl-plugin-test/" + fileName), StandardCharsets.UTF_8).toUpperCase(Locale.ROOT);
+		assertThat(fileName, contents, containsString("CREATE SEQUENCE"));
+	}
+
+
+}

hapi-tinder-plugin/src/test/java/ca/uhn/fhir/tinder/ddl/test/ExampleEntity.java

@@ -0,0 +1,25 @@
+package ca.uhn.fhir.tinder.ddl.test;
+
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.SequenceGenerator;
+import jakarta.persistence.Table;
+
+@Table()
+@Entity()
+public class ExampleEntity {
+
+	@Id
+	@SequenceGenerator(name = "SEQ_RESOURCE_HISTORY_ID", sequenceName = "SEQ_RESOURCE_HISTORY_ID")
+	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_RESOURCE_HISTORY_ID")
+	@Column(name = "PID")
+	private Long myId;
+
+	@Column(name = "RES_ID", nullable = false, updatable = false, insertable = false)
+	private Long myResourceId;
+
+
+}

pom.xml

@@ -2188,7 +2188,21 @@
 				<groupId>org.testcontainers</groupId>
 				<artifactId>testcontainers</artifactId>
 				<version>${testcontainers_version}</version>
-				<scope>test</scope>
+			</dependency>
+			<dependency>
+				<groupId>org.testcontainers</groupId>
+				<artifactId>postgresql</artifactId>
+				<version>${testcontainers_version}</version>
+			</dependency>
+			<dependency>
+				<groupId>org.testcontainers</groupId>
+				<artifactId>mssqlserver</artifactId>
+				<version>${testcontainers_version}</version>
+			</dependency>
+			<dependency>
+				<groupId>org.testcontainers</groupId>
+				<artifactId>oracle-xe</artifactId>
+				<version>${testcontainers_version}</version>
 			</dependency>
 			<dependency>
 				<groupId>org.testcontainers</groupId>
@@ -2343,7 +2357,7 @@
 						<maxmem>2000m</maxmem>
 						<compilerArgs>
 							<arg>-XDcompilePolicy=simple</arg>
-							<arg>-Xplugin:ErrorProne -Xep:MissingSummary:OFF</arg>
+							<arg>-Xplugin:ErrorProne -Xep:MissingSummary:OFF -XepExcludedPaths:.*/src/test/java/.*</arg>
 							<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.api=ALL-UNNAMED</arg>
 							<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.file=ALL-UNNAMED</arg>
 							<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.main=ALL-UNNAMED</arg>