Transaction processing improvements (#6874)

* Add junk ine

* Add extension for placeholder ID

* Cleanup

* Header

* Cleanup

* Spotless

* Better logging

* Fix transaction conditional URL prefetch on non-token params

* Drop a check

* Adjust query counts

* Improve performance

* Single token optimized

* Test fixes

* About to try to ensure we prefetch resource bodies for conditional create

* Test fixes

* Some test fixes

* Test fixes

* Test fixes

* Test fixes

* Work on tests

* Test fix

* Spotless

* Add docs

* Add test

* Add grouping

* Spotless

* Add size option to CMD

* Adjust consumer

* Cleanup

* Work on bulk import

* Spotless

* More work

* Add logging

* More diagnostics

* add logs

* Cleanup

* Fix premature finishing of bulk import command

* Add changelogs

* Test cleanup

* Test fixes

* Fix tests

* Test fix

* Spotless

* Cleanup

* Resolve conflicts

* Clean up

* Add to transaction response parser

* TransactionUtil parsing improvements

* Work on tests

* Test fix

* Test fixes

* Spotless

* Bug fix

* Build tweak

* Test cleanup

* Add some test logging

* Bump to trigger CI

* Try to address intermittent

* Address review comments

* Version bump

* License header

Author: jamesagnew

hapi-deployable-pom/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		 <groupId>ca.uhn.hapi.fhir</groupId>
 		 <artifactId>hapi-fhir</artifactId>
-		 <version>8.3.2-SNAPSHOT</version>
+		 <version>8.3.3-SNAPSHOT</version>
 
 		 <relativePath>../pom.xml</relativePath>
 	 </parent>

hapi-fhir-android/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>8.3.2-SNAPSHOT</version>
+		<version>8.3.3-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>8.3.2-SNAPSHOT</version>
+		<version>8.3.3-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/StorageResponseCodeEnum.java

@@ -51,6 +51,7 @@ public enum StorageResponseCodeEnum implements ICodingEnum {
 	SUCCESSFUL_CONDITIONAL_PATCH_NO_CHANGE(
 			"Conditional patch succeeded: No changes were detected so no action was taken."),
 	AUTOMATICALLY_CREATED_PLACEHOLDER_RESOURCE("Automatically created placeholder resource."),
+	FAILURE("Failed to process resource."),
 	;
 
 	public static final String SYSTEM = "https://hapifhir.io/fhir/CodeSystem/hapi-fhir-storage-response-code";

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

@@ -194,6 +194,13 @@ public class HapiExtensions {
 	public static final String EXTENSION_SEARCHPARAM_CUSTOM_TARGET_RESOURCE =
 			"http://hl7.org/fhir/tools/CustomTargetResource";
 
+	/**
+	 * When an OperationOutcome returned by the JPA server includes a declaration that a placeholder
+	 * reference was automatically created, this extension indicates the ID of the placeholder.
+	 */
+	public static final String EXTENSION_PLACEHOLDER_ID =
+			"http://hapifhir.io/fhir/StructureDefinition/oo-placeholder-id";
+
 	/**
 	 * When a resource is replacing another resource, this extension can be added
 	 * to include a reference to the resource that is being replaced.

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

@@ -2,11 +2,21 @@
 
 /*-
  * #%L
- * Smile CDR - CDR
+ * HAPI FHIR - Core Library
  * %%
- * Copyright (C) 2016 - 2025 Smile CDR, Inc.
+ * Copyright (C) 2014 - 2025 Smile CDR, Inc.
  * %%
- * All rights reserved.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  * #L%
  */
 

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

@@ -53,6 +53,13 @@ public static String cleanProvenanceSourceUriOrEmpty(String theProvenanceSourceU
 		return StringUtils.substringBefore(sanitizedProvenance, "#");
 	}
 
+	/**
+	 * @since 8.2.0
+	 */
+	public static String getSource(FhirContext theContext, IBaseResource theResource) {
+		return getSource(theContext, theResource.getMeta());
+	}
+
 	public static String getSource(FhirContext theContext, IBaseMetaType theMeta) {
 		if (theContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.R4)) {
 			return getSourceR4Plus(theContext, theMeta);

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

@@ -47,28 +47,30 @@ public class OperationOutcomeUtil {
 
 	/**
 	 * Add an issue to an OperationOutcome
-	 *  @param theCtx              The fhir context
+	 *
+	 * @param theCtx              The fhir context
 	 * @param theOperationOutcome The OO resource to add to
 	 * @param theSeverity         The severity (fatal | error | warning | information)
-	 * @param theDetails          The details string
+	 * @param theDiagnostics      The diagnostics string (this was called "details" in FHIR DSTU2 but was renamed to diagnostics in DSTU3)
 	 * @param theCode
 	 * @return Returns the newly added issue
 	 */
 	public static IBase addIssue(
 			FhirContext theCtx,
 			IBaseOperationOutcome theOperationOutcome,
 			String theSeverity,
-			String theDetails,
+			String theDiagnostics,
 			String theLocation,
 			String theCode) {
-		return addIssue(theCtx, theOperationOutcome, theSeverity, theDetails, theLocation, theCode, null, null, null);
+		return addIssue(
+				theCtx, theOperationOutcome, theSeverity, theDiagnostics, theLocation, theCode, null, null, null);
 	}
 
 	public static IBase addIssue(
 			FhirContext theCtx,
 			IBaseOperationOutcome theOperationOutcome,
 			String theSeverity,
-			String theDetails,
+			String theDiagnostics,
 			String theLocation,
 			String theCode,
 			@Nullable String theDetailSystem,
@@ -79,7 +81,7 @@ public static IBase addIssue(
 				theCtx,
 				issue,
 				theSeverity,
-				theDetails,
+				theDiagnostics,
 				theLocation,
 				theCode,
 				theDetailSystem,
@@ -101,7 +103,7 @@ private static IBase createIssue(FhirContext theCtx, IBaseResource theOutcome) {
 
 	/**
 	 * @deprecated Use {@link #getFirstIssueDiagnostics(FhirContext, IBaseOperationOutcome)} instead. This
-	 * method has always been misnamed for historical reasons.
+	 * 	method has always been misnamed for historical reasons.
 	 */
 	@Deprecated(forRemoval = true, since = "8.2.0")
 	public static String getFirstIssueDetails(FhirContext theCtx, IBaseOperationOutcome theOutcome) {
@@ -199,7 +201,7 @@ private static void populateDetails(
 			FhirContext theCtx,
 			IBase theIssue,
 			String theSeverity,
-			String theDetails,
+			String theDiagnostics,
 			String theLocation,
 			String theCode,
 			String theDetailSystem,
@@ -225,7 +227,7 @@ private static void populateDetails(
 		severityChild.getMutator().addValue(theIssue, severityElem);
 
 		IPrimitiveType<?> string = (IPrimitiveType<?>) stringDef.newInstance();
-		string.setValueAsString(theDetails);
+		string.setValueAsString(theDiagnostics);
 		diagnosticsChild.getMutator().setValue(theIssue, string);
 
 		addLocationToIssue(theCtx, theIssue, theLocation);

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

@@ -282,10 +282,34 @@ public String toString() {
 	}
 
 	/**
-	 * Format a throughput number (output does not include units)
+	 * Format a throughput number (output does not include units) into
+	 * a number suitable for logging.
+	 * <p>
+	 * This method tries to use a suitable amount of precision for logging.
+	 * For numbers above 1000 it includes no decimal.
+	 * For numbers between 100 and 1000 it includes one decimal.
+	 * For numbers below 100 it includes two decimals.
+	 * </p>
 	 */
 	public static String formatThroughput(double throughput) {
-		return new DecimalFormat("0.0").format(throughput);
+		return formatDouble(throughput);
+	}
+
+	/**
+	 * This method tries to use a suitable amount of precision for logging.
+	 * For numbers above 1000 it includes no decimal.
+	 * For numbers between 100 and 1000 it includes one decimal.
+	 * For numbers below 100 it includes two decimals.
+	 */
+	static String formatDouble(double theDouble) {
+		double abs = Math.abs(theDouble);
+		if (abs > 1000) {
+			return Long.toString(Math.round(theDouble));
+		}
+		if (abs > 100) {
+			return Double.toString(Math.round(theDouble * 10.0) / 10.0);
+		}
+		return Double.toString(Math.round(theDouble * 100.0) / 100.0);
 	}
 
 	/**

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

@@ -3,6 +3,8 @@
 import org.apache.commons.lang3.time.DateUtils;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.CsvSource;
 
 import java.util.Date;
 import java.util.concurrent.TimeUnit;
@@ -288,4 +290,20 @@ public void testAppendRightAlignedNumber() {
 		assertEquals("PFX0000000100", b.toString());
 	}
 
+	@ParameterizedTest
+	@CsvSource({
+		"0             , 0.0    ",
+		"1.2345        , 1.23   ",
+		"-1.2345       , -1.23   ",
+		"99.88888      , 99.89  ",
+		"-99.88888     , -99.89  ",
+		"101.88888     , 101.9  ",
+		"-101.88888    , -101.9  ",
+		"1001.88888    , 1002   ",
+		"-1001.88888   , -1002   ",
+	})
+	public void testFormatDouble(double theInput, String theExpected) {
+		assertEquals(theExpected, StopWatch.formatDouble(theInput));
+	}
+
 }