diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/SleepUtil.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/SleepUtil.java
new file mode 100644
index 00000000000..635bfae71bc
--- /dev/null
+++ b/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);
+ }
+ }
+ }
+}
diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/TestUtil.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/TestUtil.java
index 36ff4c3f536..32b725f8f4c 100644
--- a/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/TestUtil.java
+++ b/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();
- 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);
- }
- }
+ ourSleepUtil.sleepAtLeast(theMillis, theLogProgress);
}
}
diff --git a/hapi-fhir-base/src/test/java/ca/uhn/fhir/util/SleepUtilTest.java b/hapi-fhir-base/src/test/java/ca/uhn/fhir/util/SleepUtilTest.java
new file mode 100644
index 00000000000..fb6cd85788c
--- /dev/null
+++ b/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);
+ }
+
+}
diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5553-deadlocks-on-mdm-clear.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5553-deadlocks-on-mdm-clear.yaml
new file mode 100644
index 00000000000..fe9f7a0bfd5
--- /dev/null
+++ b/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."
diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5555-avoid-resource-lob-column.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5555-avoid-resource-lob-column.yaml
new file mode 100644
index 00000000000..8ae0b2fab63
--- /dev/null
+++ b/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."
diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirCockroachDialect.java b/hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirCockroachDialect.java
similarity index 100%
rename from hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirCockroachDialect.java
rename to hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirCockroachDialect.java
diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirDerbyDialect.java b/hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirDerbyDialect.java
similarity index 100%
rename from hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirDerbyDialect.java
rename to hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirDerbyDialect.java
diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirH2Dialect.java b/hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirH2Dialect.java
similarity index 95%
rename from hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirH2Dialect.java
rename to hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirH2Dialect.java
index 5cdf1eaad26..12e2f9af6be 100644
--- a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirH2Dialect.java
+++ b/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 ResourceTable#getFhirVersion()
* would look like:
*
* RES_VERSION varchar(7) check (RES_VERSION in ('DSTU2','DSTU2_HL7ORG','DSTU2_1','DSTU3','R4','R4B','R5')),
diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirMariaDBDialect.java b/hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirMariaDBDialect.java
similarity index 100%
rename from hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirMariaDBDialect.java
rename to hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirMariaDBDialect.java
diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirMySQLDialect.java b/hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirMySQLDialect.java
similarity index 100%
rename from hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirMySQLDialect.java
rename to hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirMySQLDialect.java
diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirOracleDialect.java b/hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirOracleDialect.java
similarity index 100%
rename from hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirOracleDialect.java
rename to hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirOracleDialect.java
diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirPostgres94Dialect.java b/hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirPostgres94Dialect.java
similarity index 100%
rename from hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirPostgres94Dialect.java
rename to hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirPostgres94Dialect.java
diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirPostgresDialect.java b/hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirPostgresDialect.java
similarity index 100%
rename from hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirPostgresDialect.java
rename to hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirPostgresDialect.java
diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirSQLServerDialect.java b/hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirSQLServerDialect.java
similarity index 100%
rename from hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirSQLServerDialect.java
rename to hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/model/dialect/HapiFhirSQLServerDialect.java
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/util/HapiEntityManagerFactoryUtil.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/util/HapiEntityManagerFactoryUtil.java
index 1a28f92db97..fe328bb5e1e 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/util/HapiEntityManagerFactoryUtil.java
+++ b/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;
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
index 3e23911c980..90ac47f982d 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
+++ b/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 extends BaseStora
theEntity.setResourceType(toResourceName(theResource));
}
- byte[] resourceBinary;
String resourceText;
ResourceEncodingEnum encoding;
boolean changed = false;
@@ -662,7 +659,6 @@ public abstract class BaseHapiFhirDao 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 extends BaseStora
theEntity.setFhirVersion(myContext.getVersion().getVersion());
HashFunction sha256 = Hashing.sha256();
- HashCode hashCode;
- String encodedResource = encodeResource(theResource, encoding, excludeElements, myContext);
- if (myStorageSettings.getInlineResourceTextBelowSize() > 0
- && 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);
- }
+ resourceText = encodeResource(theResource, encoding, excludeElements, myContext);
+ encoding = ResourceEncodingEnum.JSON;
+ HashCode hashCode = sha256.hashUnencodedChars(resourceText);
String hashSha256 = hashCode.toString();
if (!hashSha256.equals(theEntity.getHashSha256())) {
@@ -710,7 +696,6 @@ public abstract class BaseHapiFhirDao extends BaseStora
} else {
encoding = null;
- resourceBinary = null;
resourceText = null;
}
@@ -728,7 +713,6 @@ public abstract class BaseHapiFhirDao extends BaseStora
changed = true;
}
- resourceBinary = null;
resourceText = null;
encoding = ResourceEncodingEnum.DEL;
}
@@ -753,46 +737,19 @@ public abstract class BaseHapiFhirDao 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 extends BaseStora
List excludeElements = new ArrayList<>(8);
getExcludedElements(historyEntity.getResourceType(), excludeElements, theResource.getMeta());
String encodedResourceString = encodeResource(theResource, encoding, excludeElements, myContext);
- byte[] resourceBinary = getResourceBinary(encoding, encodedResourceString);
- boolean changed = !Arrays.equals(historyEntity.getResource(), resourceBinary);
+ boolean changed = !StringUtils.equals(historyEntity.getResourceTextVc(), encodedResourceString);
historyEntity.setUpdated(theTransactionDetails.getTransactionDate());
@@ -1450,19 +1406,14 @@ public abstract class BaseHapiFhirDao extends BaseStora
return historyEntity;
}
- if (getStorageSettings().getInlineResourceTextBelowSize() > 0
- && encodedResourceString.length() < getStorageSettings().getInlineResourceTextBelowSize()) {
- populateEncodedResource(encodedResource, encodedResourceString, null, ResourceEncodingEnum.JSON);
- } else {
- populateEncodedResource(encodedResource, null, resourceBinary, encoding);
- }
+ populateEncodedResource(encodedResource, encodedResourceString, ResourceEncodingEnum.JSON);
}
+
/*
* 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 extends BaseStora
}
private void populateEncodedResource(
- EncodedResource encodedResource,
- String encodedResourceString,
- byte[] theResourceBinary,
- ResourceEncodingEnum theEncoding) {
+ EncodedResource encodedResource, String encodedResourceString, ResourceEncodingEnum theEncoding) {
encodedResource.setResourceText(encodedResourceString);
- encodedResource.setResourceBinary(theResourceBinary);
encodedResource.setEncoding(theEncoding);
}
@@ -1542,7 +1489,6 @@ public abstract class BaseHapiFhirDao 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());
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
index dbb35bb4967..7120599b146 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
@@ -1689,19 +1689,17 @@ public abstract class BaseHapiFhirResourceDao 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
- && resourceText.length() < myStorageSettings.getInlineResourceTextBelowSize()) {
- ourLog.debug(
- "Storing text of resource {} version {} as inline VARCHAR",
- entity.getResourceId(),
- historyEntity.getVersion());
- historyEntity.setResourceTextVc(resourceText);
- historyEntity.setResource(null);
- historyEntity.setEncoding(ResourceEncodingEnum.JSON);
- changed = true;
- }
+ ourLog.debug(
+ "Storing text of resource {} version {} as inline VARCHAR",
+ entity.getResourceId(),
+ historyEntity.getVersion());
+ historyEntity.setResourceTextVc(resourceText);
+ historyEntity.setEncoding(ResourceEncodingEnum.JSON);
+ changed = true;
}
}
if (isBlank(historyEntity.getSourceUri()) && isBlank(historyEntity.getRequestId())) {
@@ -2071,6 +2069,7 @@ public abstract class BaseHapiFhirResourceDao extends B
});
}
+ @Override
public > Stream searchForIdStream(
SearchParameterMap theParams,
RequestDetails theRequest,
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/EncodedResource.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/EncodedResource.java
index 7695b44ca13..503a85b15d1 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/EncodedResource.java
+++ b/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;
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IResourceHistoryTableDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IResourceHistoryTableDao.java
index b74a1b757f2..00eeccb7345 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IResourceHistoryTableDao.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IResourceHistoryTableDao.java
@@ -79,4 +79,16 @@ public interface IResourceHistoryTableDao extends JpaRepositoryRES_TEXT_VC column to the legacy RES_TEXT 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);
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
index 12cf705407a..dcc7c9b9c6d 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
@@ -1555,11 +1555,12 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks {
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
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/entity/GeneratedSchemaTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/entity/GeneratedSchemaTest.java
new file mode 100644
index 00000000000..bd10ad84d05
--- /dev/null
+++ b/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));
+ }
+
+}
diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceHistoryTable.java b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceHistoryTable.java
index 7e951765439..0d1e0f8adaa 100644
--- a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceHistoryTable.java
+++ b/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 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)
- @JdbcTypeCode(SqlTypes.LONG32VARCHAR)
+ @Column(name = "RES_TEXT_VC", nullable = true, length = Length.LONG32)
@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;
diff --git a/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/bulk/imprt2/ConsumeFilesStepR4Test.java b/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/bulk/imprt2/ConsumeFilesStepR4Test.java
index d9208ba6ab2..5462f896a3c 100644
--- a/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/bulk/imprt2/ConsumeFilesStepR4Test.java
+++ b/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
diff --git a/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CreateTest.java b/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CreateTest.java
index 1fe09812342..db30329cbad 100644
--- a/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CreateTest.java
+++ b/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
diff --git a/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4InlineResourceModeTest.java b/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4InlineResourceModeTest.java
index 368519202f8..b37be63bfb5 100644
--- a/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4InlineResourceModeTest.java
+++ b/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.api.model.DaoMethodOutcome;
+import ca.uhn.fhir.jpa.dao.GZipUtil;
+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 org.hl7.fhir.r4.model.IdType;
+import ca.uhn.fhir.rest.param.DateRangeParam;
+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() {
- Patient patient = new Patient();
- patient.setActive(true);
- Long resourceId = myPatientDao.create(patient).getId().getIdPartAsLong();
+ public void testRetrieveNonInlinedResource() {
+ IIdType id = createPatient(withActiveTrue());
+ Long pid = id.getIdPartAsLong();
- patient = new Patient();
- patient.setId("Patient/" + resourceId);
- patient.setActive(false);
- myPatientDao.update(patient);
+ relocateResourceTextToCompressedColumn(pid, 1L);
- runInTransaction(() -> {
- // Version 1
- ResourceHistoryTable entity = myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(resourceId, 1);
- assertNull(entity.getResource());
- assertThat(entity.getResourceTextVc(), containsString("\"active\":true"));
- // Version 2
- entity = myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(resourceId, 2);
- assertNull(entity.getResource());
- assertThat(entity.getResourceTextVc(), containsString("\"active\":false"));
+ runInTransaction(()->{
+ ResourceHistoryTable historyEntity = myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(pid, 1);
+ assertNotNull(historyEntity.getResource());
+ assertNull(historyEntity.getResourceTextVc());
+ assertEquals(ResourceEncodingEnum.JSONC, historyEntity.getEncoding());
});
- patient = myPatientDao.read(new IdType("Patient/" + resourceId));
- assertFalse(patient.getActive());
+ // Read
+ validatePatient(myPatientDao.read(id.withVersion(null), mySrd));
- patient = (Patient) myPatientDao.search(SearchParameterMap.newSynchronous()).getAllResources().get(0);
- assertFalse(patient.getActive());
+ // VRead
+ 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
- public void testDontUseInlineAboveThreshold() {
- 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());
-
+ private void validatePatient(IBaseResource theRead) {
+ assertTrue(((Patient)theRead).getActive());
}
diff --git a/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4QueryCountTest.java b/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4QueryCountTest.java
index fb828747880..a65e6075ca3 100644
--- a/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4QueryCountTest.java
+++ b/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
- " false, false, CURRENT_VERSION, 2, 1",
- " true, false, CURRENT_VERSION, 2, 0",
- " false, true, CURRENT_VERSION, 12, 1",
- " true, true, CURRENT_VERSION, 12, 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",
+ // OptimisticLock OptimizeMode ExpectedSelect ExpectedUpdate
+ " false, CURRENT_VERSION, 2, 0",
+ " true, CURRENT_VERSION, 12, 0",
+ " false, ALL_VERSIONS, 12, 0",
+ " 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++) {
diff --git a/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java b/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java
index 569ff1aad7c..649359d3937 100644
--- a/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java
+++ b/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);
}
diff --git a/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4Test.java b/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4Test.java
index 9d48781b40b..93dc9dfc6e3 100644
--- a/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4Test.java
+++ b/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) t -> {
ResourceHistoryTable resourceHistoryTable = myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(id.getIdPartAsLong(), id.getVersionIdPartAsLong());
resourceHistoryTable.setEncoding(ResourceEncodingEnum.JSON);
- try {
- resourceHistoryTable.setResource("{\"resourceType\":\"FOO\"}".getBytes("UTF-8"));
- } catch (UnsupportedEncodingException e) {
- throw new Error(e);
- }
+ resourceHistoryTable.setResourceTextVc("{\"resourceType\":\"FOO\"}");
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");
diff --git a/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java b/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java
index b53ac1ef305..77cbd0d21ce 100644
--- a/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java
+++ b/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 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 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);
diff --git a/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderInvalidDataR4Test.java b/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderInvalidDataR4Test.java
index 52a3e23accf..b16956171b9 100644
--- a/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderInvalidDataR4Test.java
+++ b/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 = GZipUtil.decompress(bytesCompressed);
+ String resourceText = resVer.getResourceTextVc();
resourceText = resourceText.replace("100", "-.100");
- bytesCompressed = GZipUtil.compress(resourceText);
- resVer.setResource(bytesCompressed);
+ resVer.setResourceTextVc(resourceText);
myResourceHistoryTableDao.save(resVer);
});
diff --git a/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java b/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
index 837a41b68a2..6c28d39348a 100644
--- a/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
+++ b/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();
diff --git a/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/stresstest/GiantTransactionPerfTest.java b/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/stresstest/GiantTransactionPerfTest.java
index 67aeca52c42..ec9d5d8a4d5 100644
--- a/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/stresstest/GiantTransactionPerfTest.java
+++ b/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 findAll() {
diff --git a/hapi-fhir-jpaserver-test-r5/pom.xml b/hapi-fhir-jpaserver-test-r5/pom.xml
index df1d9fc41e3..eb2a7a64796 100644
--- a/hapi-fhir-jpaserver-test-r5/pom.xml
+++ b/hapi-fhir-jpaserver-test-r5/pom.xml
@@ -34,6 +34,20 @@
test
+
+
+ junit
+ junit
+ 4.13.2
+ provided
+
+
+ org.hamcrest
+ hamcrest-core
+
+
+
+
diff --git a/hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/database/BaseDatabaseVerificationIT.java b/hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/database/BaseDatabaseVerificationIT.java
new file mode 100644
index 00000000000..bfc75f33643
--- /dev/null
+++ b/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 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;
+ }
+ }
+
+
+}
+
+
diff --git a/hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/database/DatabaseVerificationWithMsSqlIT.java b/hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/database/DatabaseVerificationWithMsSqlIT.java
new file mode 100644
index 00000000000..a6cf07f394d
--- /dev/null
+++ b/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()
+ );
+ }
+ }
+
+
+}
diff --git a/hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/database/DatabaseVerificationWithOracleIT.java b/hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/database/DatabaseVerificationWithOracleIT.java
new file mode 100644
index 00000000000..d2c72605d6c
--- /dev/null
+++ b/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()
+ );
+ }
+ }
+
+
+}
diff --git a/hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/database/DatabaseVerificationWithPostgresIT.java b/hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/database/DatabaseVerificationWithPostgresIT.java
new file mode 100644
index 00000000000..7bf2a5712b9
--- /dev/null
+++ b/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()
+ );
+ }
+ }
+
+
+}
diff --git a/hapi-fhir-jpaserver-test-utilities/ResourceTable/segments_1 b/hapi-fhir-jpaserver-test-utilities/ResourceTable/segments_1
new file mode 100644
index 00000000000..45ec119a611
Binary files /dev/null and b/hapi-fhir-jpaserver-test-utilities/ResourceTable/segments_1 differ
diff --git a/hapi-fhir-jpaserver-test-utilities/ResourceTable/write.lock b/hapi-fhir-jpaserver-test-utilities/ResourceTable/write.lock
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/hapi-fhir-jpaserver-test-utilities/TermConcept/segments_1 b/hapi-fhir-jpaserver-test-utilities/TermConcept/segments_1
new file mode 100644
index 00000000000..bebbd510042
Binary files /dev/null and b/hapi-fhir-jpaserver-test-utilities/TermConcept/segments_1 differ
diff --git a/hapi-fhir-jpaserver-test-utilities/TermConcept/write.lock b/hapi-fhir-jpaserver-test-utilities/TermConcept/write.lock
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/hapi-fhir-jpaserver-test-utilities/pom.xml b/hapi-fhir-jpaserver-test-utilities/pom.xml
index 9a2166c22ea..225aae4f29f 100644
--- a/hapi-fhir-jpaserver-test-utilities/pom.xml
+++ b/hapi-fhir-jpaserver-test-utilities/pom.xml
@@ -131,20 +131,14 @@
org.testcontainers
postgresql
- 1.17.6
- compile
org.testcontainers
mssqlserver
- 1.17.6
- compile
org.testcontainers
oracle-xe
- 1.17.6
- compile
org.postgresql
diff --git a/hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/embedded/JpaEmbeddedDatabase.java b/hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/embedded/JpaEmbeddedDatabase.java
index ae26426bdee..f87d1d25d14 100644
--- a/hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/embedded/JpaEmbeddedDatabase.java
+++ b/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();
diff --git a/hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/BaseJpaR4Test.java b/hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/BaseJpaR4Test.java
index 68813b7c4d5..9515d61bbe7 100644
--- a/hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/BaseJpaR4Test.java
+++ b/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);
diff --git a/hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/config/TestR5Config.java b/hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/config/TestR5Config.java
index 10ca0859722..828bd153d1c 100644
--- a/hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/config/TestR5Config.java
+++ b/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");
diff --git a/hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/ColumnTypeEnum.java b/hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/ColumnTypeEnum.java
index 8c894e824c6..d1306fbe103 100644
--- a/hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/ColumnTypeEnum.java
+++ b/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:
- * @JdbcTypeCode(SqlTypes.LONG32VARCHAR)
+ * @Column(length=Integer.MAX_VALUE)
*/
TEXT,
BIG_DECIMAL;
diff --git a/hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/ColumnTypeToDriverTypeToSqlType.java b/hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/ColumnTypeToDriverTypeToSqlType.java
index 97ec7c8c673..f64c34554c0 100644
--- a/hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/ColumnTypeToDriverTypeToSqlType.java
+++ b/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");
diff --git a/hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/api/config/JpaStorageSettings.java b/hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/api/config/JpaStorageSettings.java
index 53faa3d2c6c..44f05007c05 100644
--- a/hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/api/config/JpaStorageSettings.java
+++ b/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 HFJ_RES_VER 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 HFJ_RES_VER 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 HFJ_RES_VER 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
}
/**
diff --git a/hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/tx/HapiTransactionService.java b/hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/tx/HapiTransactionService.java
index 990ef103309..719d8891b34 100644
--- a/hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/tx/HapiTransactionService.java
+++ b/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 theClass) {
+ return ExceptionUtils.indexOfType(theThrowable, theClass) != -1;
+ }
+
+ private boolean isThrowablePresent(Throwable theThrowable, Class 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 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
- || ExceptionUtils.indexOfThrowable(e, DataIntegrityViolationException.class) != -1
- || ExceptionUtils.indexOfThrowable(e, ConstraintViolationException.class) != -1
- || ExceptionUtils.indexOfThrowable(e, ObjectOptimisticLockingFailureException.class)
- != -1)) {
+ if (!isRetriable(e)) {
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.",
diff --git a/hapi-fhir-storage/src/test/java/ca/uhn/fhir/jpa/dao/tx/HapiTransactionServiceTest.java b/hapi-fhir-storage/src/test/java/ca/uhn/fhir/jpa/dao/tx/HapiTransactionServiceTest.java
new file mode 100644
index 00000000000..1547cf2114d
--- /dev/null
+++ b/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 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 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 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());
+ }
+}
diff --git a/hapi-fhir-test-utilities/src/main/java/ca/uhn/fhir/test/utilities/jpa/JpaModelScannerAndVerifier.java b/hapi-fhir-test-utilities/src/main/java/ca/uhn/fhir/test/utilities/jpa/JpaModelScannerAndVerifier.java
index 47810c38c1a..94d4fd93943 100644
--- a/hapi-fhir-test-utilities/src/main/java/ca/uhn/fhir/test/utilities/jpa/JpaModelScannerAndVerifier.java
+++ b/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);
diff --git a/hapi-tinder-plugin/pom.xml b/hapi-tinder-plugin/pom.xml
index 7346ec210df..310dbbcd3b4 100644
--- a/hapi-tinder-plugin/pom.xml
+++ b/hapi-tinder-plugin/pom.xml
@@ -184,14 +184,6 @@
org.apache.maven
maven-plugin-api
-
org.apache.maven.plugin-tools
diff --git a/hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/ddl/DdlGeneratorHibernate61.java b/hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/ddl/DdlGeneratorHibernate61.java
index f304d194fc9..a60af7c015f 100644
--- a/hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/ddl/DdlGeneratorHibernate61.java
+++ b/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)
- 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);
- }
- }
+ IoUtil.closeQuietly(connectionProvider);
}
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 Connection getConnection() throws SQLException {
- ourLog.trace("Using internal driver: {}", org.h2.Driver.class);
- return DriverManager.getConnection("jdbc:h2:mem:tmp", "sa", "sa");
+ public FakeConnectionConnectionProvider() {
+ try {
+ connection = 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 {
- conn.close();
+ public Connection getConnection() {
+ 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);
+ }
}
}
}
diff --git a/hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/ddl/GenerateDdlMojo.java b/hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/ddl/GenerateDdlMojo.java
index 9d3dc65b5fa..a8739463519 100644
--- a/hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/ddl/GenerateDdlMojo.java
+++ b/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 packageNames;
+ List packageNames;
@Parameter
- private List dialects;
+ List 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:
*
* ca.uhn.hapi.fhir
* hapi-fhir-jpaserver-model
* ${project.version}
*
+ *
+ * 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();
}
diff --git a/hapi-tinder-plugin/src/test/java/ca/uhn/fhir/tinder/ddl/GenerateDdlMojoTest.java b/hapi-tinder-plugin/src/test/java/ca/uhn/fhir/tinder/ddl/GenerateDdlMojoTest.java
new file mode 100644
index 00000000000..88af72a4b9e
--- /dev/null
+++ b/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"));
+ }
+
+
+}
diff --git a/hapi-tinder-plugin/src/test/java/ca/uhn/fhir/tinder/ddl/test/ExampleEntity.java b/hapi-tinder-plugin/src/test/java/ca/uhn/fhir/tinder/ddl/test/ExampleEntity.java
new file mode 100644
index 00000000000..9c400c45a90
--- /dev/null
+++ b/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;
+
+
+}
diff --git a/pom.xml b/pom.xml
index 9c84fe29e1c..8c52e0c4f79 100644
--- a/pom.xml
+++ b/pom.xml
@@ -2188,7 +2188,21 @@
org.testcontainers
testcontainers
${testcontainers_version}
- test
+
+
+ org.testcontainers
+ postgresql
+ ${testcontainers_version}
+
+
+ org.testcontainers
+ mssqlserver
+ ${testcontainers_version}
+
+
+ org.testcontainers
+ oracle-xe
+ ${testcontainers_version}
org.testcontainers
@@ -2343,7 +2357,7 @@
2000m
-XDcompilePolicy=simple
- -Xplugin:ErrorProne -Xep:MissingSummary:OFF
+ -Xplugin:ErrorProne -Xep:MissingSummary:OFF -XepExcludedPaths:.*/src/test/java/.*
-J--add-exports=jdk.compiler/com.sun.tools.javac.api=ALL-UNNAMED
-J--add-exports=jdk.compiler/com.sun.tools.javac.file=ALL-UNNAMED
-J--add-exports=jdk.compiler/com.sun.tools.javac.main=ALL-UNNAMED