Add Bulk Patch and Bulk Patch Rewrite Jobs (#7186)

* Work on task

* Work on reindex

* Work on batch job

* Add job

* Work on feature

* Job almost working

* Tests passing

* Compile fixes

* Test fix

* Build fix

* Fix test issues

* Formatting

* Work on reindex

* Test fixes

* Disable bulk patch by default

* Add xtensibility

* Cleanup

* Add changelog

* Test fixes

* Build fixes

* Build fix

* Add message code

* Address review comments

* Version bump

* Add test utilities

* Spotless

Author: jamesagnew

hapi-deployable-pom/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		 <groupId>ca.uhn.hapi.fhir</groupId>
 		 <artifactId>hapi-fhir</artifactId>
-		 <version>8.5.1-SNAPSHOT</version>
+		 <version>8.5.2-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>8.5.1-SNAPSHOT</version>
+		<version>8.5.2-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>8.5.1-SNAPSHOT</version>
+		<version>8.5.2-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/exceptions/ResourceGoneException.java

@@ -27,7 +27,7 @@
 import org.hl7.fhir.instance.model.api.IIdType;
 
 /**
- * Represents an <b>HTTP 410 Resource Gone</b> response, which geenerally
+ * Represents an <b>HTTP 410 Resource Gone</b> response, which generally
  * indicates that the resource has been deleted
  */
 @CoverageIgnore

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

@@ -24,6 +24,7 @@
 import ca.uhn.fhir.context.FhirContext;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
+import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
@@ -61,6 +62,7 @@ public class CanonicalBundleEntry {
 
 	// Link fields (less common but part of spec)
 	private List<Map<String, String>> myLinks;
+	private IBaseOperationOutcome myResponseOutcome;
 
 	public CanonicalBundleEntry() {
 		// Default constructor
@@ -186,6 +188,14 @@ public void setLinks(List<Map<String, String>> theLinks) {
 		myLinks = theLinks;
 	}
 
+	public void setResponseOutcome(IBaseOperationOutcome theResponseOutcome) {
+		myResponseOutcome = theResponseOutcome;
+	}
+
+	public IBaseOperationOutcome getResponseOutcome() {
+		return myResponseOutcome;
+	}
+
 	/**
 	 * Factory method to create a CanonicalBundleEntry from a Bundle Entry
 	 * @param theFhirContext The FHIR context
@@ -267,6 +277,12 @@ public static CanonicalBundleEntry fromBundleEntry(FhirContext theFhirContext, I
 			if (lastModified != null) {
 				retVal.setResponseLastModified(lastModified.getValueAsString());
 			}
+
+			IBaseOperationOutcome outcome =
+					terser.getSingleValueOrNull(response, "outcome", IBaseOperationOutcome.class);
+			if (outcome != null) {
+				retVal.setResponseOutcome(outcome);
+			}
 		}
 
 		// Extract search fields
@@ -453,6 +469,13 @@ public <T extends IBase> T toBundleEntry(FhirContext theFhirContext, Class<T> th
 						lastModifiedChild.getMutator().setValue(response, lastModifiedValue);
 					}
 				}
+
+				if (myResponseOutcome != null) {
+					BaseRuntimeChildDefinition outcomeChild = responseDef.getChildByName("outcome");
+					if (outcomeChild != null) {
+						outcomeChild.getMutator().setValue(response, myResponseOutcome);
+					}
+				}
 			}
 		}
 

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

@@ -51,14 +51,28 @@ public class OperationOutcomeUtil {
 	public static final String OO_SEVERITY_WARN = "warning";
 	public static final String OO_ISSUE_CODE_INFORMATIONAL = "informational";
 
+	/**
+	 * Note: This code was added in FHIR R5, so the {@link #addIssue(FhirContext, IBaseOperationOutcome, String, String, String, String) addIssue}
+	 * methods here will automatically convert it to {@link #OO_ISSUE_CODE_INFORMATIONAL} for
+	 * previous versions of FHIR.
+	 *
+	 * @since 8.6.0
+	 */
+	public static final String OO_ISSUE_CODE_SUCCESS = "success";
+
+	/**
+	 * @since 8.6.0
+	 */
+	public static final String OO_ISSUE_CODE_PROCESSING = "processing";
+
 	/**
 	 * Add an issue to an OperationOutcome
 	 *
 	 * @param theCtx              The fhir context
 	 * @param theOperationOutcome The OO resource to add to
 	 * @param theSeverity         The severity (fatal | error | warning | information)
 	 * @param theDiagnostics      The diagnostics string (this was called "details" in FHIR DSTU2 but was renamed to diagnostics in DSTU3)
-	 * @param theCode
+	 * @param theCode             A code, such as {@link #OO_ISSUE_CODE_INFORMATIONAL} or {@link #OO_ISSUE_CODE_SUCCESS}
 	 * @return Returns the newly added issue
 	 */
 	public static IBase addIssue(
@@ -221,7 +235,13 @@ private static void populateDetails(
 		BaseRuntimeChildDefinition codeChild = issueElement.getChildByName("code");
 		IPrimitiveType<?> codeElem = (IPrimitiveType<?>)
 				codeChild.getChildByName("code").newInstance(codeChild.getInstanceConstructorArguments());
-		codeElem.setValueAsString(theCode);
+		String code = theCode;
+		if (theCtx.getVersion().getVersion().isOlderThan(FhirVersionEnum.R5) && "success".equals(code)) {
+			// "success" was added in R5 so we switch back to "informational" for older versions
+			code = "informational";
+		}
+
+		codeElem.setValueAsString(code);
 		codeChild.getMutator().addValue(theIssue, codeElem);
 
 		BaseRuntimeElementDefinition<?> stringDef = diagnosticsChild.getChildByName(diagnosticsChild.getElementName());

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

@@ -27,6 +27,8 @@
 import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.model.api.annotation.Description;
 import ca.uhn.fhir.model.primitive.StringDt;
+import com.google.common.collect.Multimap;
+import com.google.common.collect.MultimapBuilder;
 import jakarta.annotation.Nullable;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBase;
@@ -46,10 +48,11 @@
 import java.util.List;
 import java.util.Objects;
 import java.util.Optional;
+import java.util.function.BiConsumer;
 import java.util.function.Function;
-import java.util.stream.Collectors;
 
 import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
+import static org.apache.commons.lang3.StringUtils.defaultString;
 import static org.apache.commons.lang3.StringUtils.isBlank;
 
 /**
@@ -137,27 +140,54 @@ public static Optional<IBase> getNamedParameter(
 				.findFirst();
 	}
 
+	/**
+	 * Returns a map containing all of the named parameters in a Parameters resource. The key will be the
+	 * <code>Parameters.parameter.name</code> value (or an empty string <code>""</code> if no name is present)
+	 * and the value will be the <code>Parameters.parameter</code> repetition.
+	 *
+	 * @param theCtx The FhirContext instance appropriate for the input
+	 * @param theParameters The Parameters resource to examine
+	 * @return A map containing named parameters
+	 * @since 8.4.0
+	 */
+	public static Multimap<String, IBase> getNamedParameters(FhirContext theCtx, IBaseResource theParameters) {
+		Multimap<String, IBase> retVal =
+				MultimapBuilder.hashKeys().arrayListValues().build();
+		BiConsumer<String, IBase> consumer = (paramName, part) -> {
+			paramName = defaultString(paramName);
+			retVal.put(paramName, part);
+		};
+
+		getNamedParameters(theCtx, theParameters, consumer);
+
+		return retVal;
+	}
+
 	public static List<IBase> getNamedParameters(
 			FhirContext theCtx, IBaseResource theParameters, String theParameterName) {
+		List<IBase> retVal = new ArrayList<>();
+		BiConsumer<String, IBase> consumer = (paramName, part) -> {
+			if (theParameterName.equals(paramName)) {
+				retVal.add(part);
+			}
+		};
+
+		getNamedParameters(theCtx, theParameters, consumer);
+
+		return retVal;
+	}
+
+	private static void getNamedParameters(
+			FhirContext theCtx, IBaseResource theParameters, BiConsumer<String, IBase> theConsumer) {
 		Validate.notNull(theParameters, "theParameters must not be null");
-		RuntimeResourceDefinition resDef = theCtx.getResourceDefinition(theParameters.getClass());
-		BaseRuntimeChildDefinition parameterChild = resDef.getChildByName("parameter");
-		List<IBase> parameterReps = parameterChild.getAccessor().getValues(theParameters);
-
-		return parameterReps.stream()
-				.filter(param -> {
-					BaseRuntimeElementCompositeDefinition<?> nextParameterDef =
-							(BaseRuntimeElementCompositeDefinition<?>) theCtx.getElementDefinition(param.getClass());
-					BaseRuntimeChildDefinition nameChild = nextParameterDef.getChildByName("name");
-					List<IBase> nameValues = nameChild.getAccessor().getValues(param);
-					Optional<? extends IPrimitiveType<?>> nameValue = nameValues.stream()
-							.filter(t -> t instanceof IPrimitiveType<?>)
-							.map(t -> ((IPrimitiveType<?>) t))
-							.findFirst();
-					return nameValue.isPresent()
-							&& theParameterName.equals(nameValue.get().getValueAsString());
-				})
-				.collect(Collectors.toList());
+
+		FhirTerser terser = theCtx.newTerser();
+		List<IBase> parameterReps = terser.getValues(theParameters, "parameter");
+
+		for (IBase parameter : parameterReps) {
+			String name = terser.getSinglePrimitiveValueOrNull(parameter, "name");
+			theConsumer.accept(name, parameter);
+		}
 	}
 
 	public static Optional<IBase> getParameterPart(FhirContext theCtx, IBase theParameter, String theParameterName) {

hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties

@@ -92,6 +92,7 @@ ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.cantUndeleteWithDeletesDisabled=Unable to re
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.incomingNoopInTransaction=Transaction contains resource with operation NOOP. This is only valid as a response operation, not in a request
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.invalidMatchUrlInvalidResourceType=Invalid match URL "{0}" - Unknown resource type: "{1}"
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.resourceTypeAndFhirIdConflictAcrossPartitions=Failed to create/update resource [{0}/{1}] in partition {2} because a resource of the same type and ID is found in another partition
+ca.uhn.fhir.jpa.dao.BaseStorageDao.updateWithHistoryRewriteDisabled=Update with history rewrite is not supported on this server
 ca.uhn.fhir.jpa.dao.BaseStorageDao.invalidMatchUrlNoMatches=Invalid match URL "{0}" - No resources match this search
 ca.uhn.fhir.jpa.dao.BaseStorageDao.invalidMatchUrlCantUseForAutoCreatePlaceholder=Invalid match URL "{0}" - No resources match this search and the URL is not valid for automatic placeholder reference target creation
 ca.uhn.fhir.jpa.dao.BaseStorageDao.inlineMatchNotSupported=Inline match URLs are not supported on this server. Cannot process reference: "{0}"
@@ -165,6 +166,7 @@ ca.uhn.fhir.jpa.search.builder.QueryStack.cantSortOnCoordParamWithoutValues=Can
 ca.uhn.fhir.jpa.search.builder.predicate.TokenPredicateBuilder.invalidCodeMissingSystem=Invalid token specified for parameter {0} - No system specified: {1}|{2}
 ca.uhn.fhir.jpa.search.builder.predicate.TokenPredicateBuilder.invalidCodeMissingCode=Invalid token specified for parameter {0} - No code specified: {1}|{2}
 
+
 ca.uhn.fhir.jpa.term.TermConceptMappingSvcImpl.matchesFound=Matches found
 ca.uhn.fhir.jpa.term.TermConceptMappingSvcImpl.noMatchesFound=No Matches found
 ca.uhn.fhir.jpa.term.TermConceptMappingSvcImpl.onlyNegativeMatchesFound=Only negative matches found

hapi-fhir-bom/pom.xml

@@ -4,15 +4,15 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>ca.uhn.hapi.fhir</groupId>
 	<artifactId>hapi-fhir-bom</artifactId>
-	<version>8.5.1-SNAPSHOT</version>
+	<version>8.5.2-SNAPSHOT</version>
 
 	<packaging>pom</packaging>
 	<name>HAPI FHIR BOM</name>
 
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>8.5.1-SNAPSHOT</version>
+		<version>8.5.2-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-checkstyle/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>8.5.1-SNAPSHOT</version>
+		<version>8.5.2-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>