Merge branch 'master' into jm-rehoming-operation

hapi-deployable-pom/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		 <groupId>ca.uhn.hapi.fhir</groupId>
 		 <artifactId>hapi-fhir</artifactId>
-		 <version>7.5.1-SNAPSHOT</version>
+		 <version>7.7.3-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>7.5.1-SNAPSHOT</version>
+		<version>7.7.3-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>7.5.1-SNAPSHOT</version>
+		<version>7.7.3-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

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

@@ -33,6 +33,7 @@ import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.concurrent.ConcurrentHashMap;
 
 public abstract class BaseRuntimeElementDefinition<T extends IBase> {
 
@@ -40,7 +41,7 @@ public abstract class BaseRuntimeElementDefinition<T extends IBase> {
 	private final Class<? extends T> myImplementingClass;
 	private final String myName;
 	private final boolean myStandardType;
-	private Map<Class<?>, Constructor<T>> myConstructors = Collections.synchronizedMap(new HashMap<>());
+	private final Map<Class<?>, Constructor<T>> myConstructors = new ConcurrentHashMap<>();
 	private List<RuntimeChildDeclaredExtensionDefinition> myExtensions = new ArrayList<>();
 	private List<RuntimeChildDeclaredExtensionDefinition> myExtensionsModifier = new ArrayList<>();
 	private List<RuntimeChildDeclaredExtensionDefinition> myExtensionsNonModifier = new ArrayList<>();
@@ -84,27 +85,24 @@ public abstract class BaseRuntimeElementDefinition<T extends IBase> {
 			argumentType = theArgument.getClass();
 		}
 
-		Constructor<T> retVal = myConstructors.get(argumentType);
+		Constructor<T> retVal = myConstructors.computeIfAbsent(argumentType, type -> {
-		if (retVal == null) {
 			for (Constructor<?> next : getImplementingClass().getConstructors()) {
-				if (argumentType == VOID_CLASS) {
+				if (type == VOID_CLASS) {
 					if (next.getParameterTypes().length == 0) {
-						retVal = (Constructor<T>) next;
+						return (Constructor<T>) next;
-						break;
-					}
-				} else if (next.getParameterTypes().length == 1) {
-					if (next.getParameterTypes()[0].isAssignableFrom(argumentType)) {
-						retVal = (Constructor<T>) next;
-						break;
 					}
+				} else if (next.getParameterTypes().length == 1 && next.getParameterTypes()[0].isAssignableFrom(type)) {
+					return (Constructor<T>) next;
 				}
 			}
-			if (retVal == null) {
+			return null;
-				throw new ConfigurationException(Msg.code(1695) + "Class " + getImplementingClass()
+		});
-						+ " has no constructor with a single argument of type " + argumentType);
+
-			}
+		if (retVal == null) {
-			myConstructors.put(argumentType, retVal);
+			throw new ConfigurationException(Msg.code(1695) + "Class " + getImplementingClass()
+					+ " has no constructor with a single argument of type " + argumentType);
 		}
+
 		return retVal;
 	}
 

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

@@ -60,6 +60,7 @@ public class RuntimeSearchParam {
 	private final List<Component> myComponents;
 	private final IIdType myIdUnqualifiedVersionless;
 	private IPhoneticEncoder myPhoneticEncoder;
+	private boolean myEnabledForSearching = true;
 
 	/**
 	 * Constructor
@@ -166,6 +167,24 @@ public class RuntimeSearchParam {
 		}
 	}
 
+	/**
+	 * Is this search parameter actually enabled for being used in searches (as opposed to only being used for
+	 * generating indexes, which might be desired while the search parameter is still being indexed). This
+	 * setting defaults to {@literal true} if it isn't set otherwise.
+	 */
+	public boolean isEnabledForSearching() {
+		return myEnabledForSearching;
+	}
+
+	/**
+	 * Is this search parameter actually enabled for being used in searches (as opposed to only being used for
+	 * generating indexes, which might be desired while the search parameter is still being indexed). This
+	 * setting defaults to {@literal true} if it isn't set otherwise.
+	 */
+	public void setEnabledForSearching(boolean theEnabledForSearching) {
+		myEnabledForSearching = theEnabledForSearching;
+	}
+
 	public List<Component> getComponents() {
 		return myComponents;
 	}
@@ -361,13 +380,6 @@ public class RuntimeSearchParam {
 		return !myUpliftRefchains.isEmpty();
 	}
 
-	public enum RuntimeSearchParamStatusEnum {
-		ACTIVE,
-		DRAFT,
-		RETIRED,
-		UNKNOWN
-	}
-
 	/**
 	 * This method tests whether a given FHIRPath expression <i>could</i>
 	 * possibly apply to the given resource type.
@@ -413,6 +425,13 @@ public class RuntimeSearchParam {
 		return false;
 	}
 
+	public enum RuntimeSearchParamStatusEnum {
+		ACTIVE,
+		DRAFT,
+		RETIRED,
+		UNKNOWN
+	}
+
 	public static class Component {
 		private final String myExpression;
 		private final String myReference;

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

@@ -727,7 +727,7 @@ public interface IValidationSupport {
 			return this;
 		}
 
-		String getCodeSystemName() {
+		public String getCodeSystemName() {
 			return myCodeSystemName;
 		}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/api/Pointcut.java

@@ -2174,6 +2174,32 @@ public enum Pointcut implements IPointcut {
 			"ca.uhn.fhir.rest.api.server.RequestDetails",
 			"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails"),
 
+	/**
+	 * <b>Storage Hook:</b>
+	 * Invoked when a partition has been deleted, typically meaning the <code>$partition-management-delete-partition</code>
+	 * operation has been invoked.
+	 * <p>
+	 * This hook will only be called if
+	 * partitioning is enabled in the JPA server.
+	 * </p>
+	 * <p>
+	 * Hooks may accept the following parameters:
+	 * </p>
+	 * <ul>
+	 * <li>
+	 * ca.uhn.fhir.interceptor.model.RequestPartitionId - The ID of the partition that was deleted.
+	 * </li>
+	 * </ul>
+	 * <p>
+	 * Hooks must return void.
+	 * </p>
+	 */
+	STORAGE_PARTITION_DELETED(
+			// Return type
+			void.class,
+			// Params
+			"ca.uhn.fhir.interceptor.model.RequestPartitionId"),
+
 	/**
 	 * <b>Storage Hook:</b>
 	 * Invoked before any partition aware FHIR operation, when the selected partition has been identified (ie. after the

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java

@@ -115,6 +115,7 @@ public class Constants {
 	public static final String HEADER_AUTHORIZATION_VALPREFIX_BASIC = "Basic ";
 	public static final String HEADER_AUTHORIZATION_VALPREFIX_BEARER = "Bearer ";
 	public static final String HEADER_CACHE_CONTROL = "Cache-Control";
+	public static final String HEADER_CLIENT_TIMEZONE = "Timezone";
 	public static final String HEADER_CONTENT_DISPOSITION = "Content-Disposition";
 	public static final String HEADER_CONTENT_ENCODING = "Content-Encoding";
 	public static final String HEADER_CONTENT_LOCATION = "Content-Location";

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/DateRangeParam.java

@@ -112,6 +112,8 @@ public class DateRangeParam implements IQueryParameterAnd<DateParam> {
 						theDateParam.setValueAsString(DateUtils.getCompletedDate(theDateParam.getValueAsString())
 								.getRight());
 					}
+					// there is only one value; we will set it as the lower bound
+					// as a >= operation
 					validateAndSet(theDateParam, null);
 					break;
 				case ENDS_BEFORE:
@@ -121,6 +123,9 @@ public class DateRangeParam implements IQueryParameterAnd<DateParam> {
 						theDateParam.setValueAsString(DateUtils.getCompletedDate(theDateParam.getValueAsString())
 								.getLeft());
 					}
+
+					// there is only one value; we will set it as the upper bound
+					// as a <= operation
 					validateAndSet(null, theDateParam);
 					break;
 				default:
@@ -318,8 +323,8 @@ public class DateRangeParam implements IQueryParameterAnd<DateParam> {
 				case NOT_EQUAL:
 					break;
 				case LESSTHAN:
-				case APPROXIMATE:
 				case LESSTHAN_OR_EQUALS:
+				case APPROXIMATE:
 				case ENDS_BEFORE:
 					throw new IllegalStateException(
 							Msg.code(1926) + "Invalid lower bound comparator: " + myLowerBound.getPrefix());
@@ -383,9 +388,9 @@ public class DateRangeParam implements IQueryParameterAnd<DateParam> {
 				case NOT_EQUAL:
 				case GREATERTHAN_OR_EQUALS:
 					break;
+				case LESSTHAN_OR_EQUALS:
 				case LESSTHAN:
 				case APPROXIMATE:
-				case LESSTHAN_OR_EQUALS:
 				case ENDS_BEFORE:
 					throw new IllegalStateException(
 							Msg.code(1928) + "Invalid lower bound comparator: " + theLowerBound.getPrefix());
@@ -470,10 +475,13 @@ public class DateRangeParam implements IQueryParameterAnd<DateParam> {
 		if (myLowerBound != null && myLowerBound.getMissing() != null) {
 			retVal.add((myLowerBound));
 		} else {
-			if (myLowerBound != null && !myLowerBound.isEmpty()) {
+			boolean hasLowerBound = myLowerBound != null && !myLowerBound.isEmpty();
+			boolean hasUpperBound = myUpperBound != null && !myUpperBound.isEmpty();
+
+			if (hasLowerBound) {
 				retVal.add((myLowerBound));
 			}
-			if (myUpperBound != null && !myUpperBound.isEmpty()) {
+			if (hasUpperBound) {
 				retVal.add((myUpperBound));
 			}
 		}

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

@@ -20,6 +20,7 @@
 package ca.uhn.fhir.util;
 
 import ca.uhn.fhir.i18n.Msg;
+import com.google.common.base.Preconditions;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.tuple.ImmutablePair;
 import org.apache.commons.lang3.tuple.Pair;
@@ -28,11 +29,20 @@ import java.lang.ref.SoftReference;
 import java.text.ParseException;
 import java.text.ParsePosition;
 import java.text.SimpleDateFormat;
+import java.time.LocalDateTime;
+import java.time.Month;
+import java.time.YearMonth;
+import java.time.format.DateTimeFormatter;
+import java.time.temporal.ChronoField;
+import java.time.temporal.TemporalAccessor;
+import java.time.temporal.TemporalField;
 import java.util.Calendar;
 import java.util.Date;
 import java.util.HashMap;
 import java.util.Locale;
 import java.util.Map;
+import java.util.Objects;
+import java.util.Optional;
 import java.util.TimeZone;
 
 /**
@@ -93,6 +103,89 @@ public final class DateUtils {
 	 */
 	private DateUtils() {}
 
+	/**
+	 * Calculate a LocalDateTime with any missing date/time data points defaulting to the earliest values (ex 0 for hour)
+	 * from a TemporalAccessor or empty if it doesn't contain a year.
+	 *
+	 * @param theTemporalAccessor The TemporalAccessor containing date/time information
+	 * @return A LocalDateTime or empty
+	 */
+	public static Optional<LocalDateTime> extractLocalDateTimeForRangeStartOrEmpty(
+			TemporalAccessor theTemporalAccessor) {
+		if (theTemporalAccessor.isSupported(ChronoField.YEAR)) {
+			final int year = theTemporalAccessor.get(ChronoField.YEAR);
+			final Month month = Month.of(getTimeUnitIfSupported(theTemporalAccessor, ChronoField.MONTH_OF_YEAR, 1));
+			final int day = getTimeUnitIfSupported(theTemporalAccessor, ChronoField.DAY_OF_MONTH, 1);
+			final int hour = getTimeUnitIfSupported(theTemporalAccessor, ChronoField.HOUR_OF_DAY, 0);
+			final int minute = getTimeUnitIfSupported(theTemporalAccessor, ChronoField.MINUTE_OF_HOUR, 0);
+			final int seconds = getTimeUnitIfSupported(theTemporalAccessor, ChronoField.SECOND_OF_MINUTE, 0);
+
+			return Optional.of(LocalDateTime.of(year, month, day, hour, minute, seconds));
+		}
+
+		return Optional.empty();
+	}
+
+	/**
+	 * Calculate a LocalDateTime with any missing date/time data points defaulting to the latest values (ex 23 for hour)
+	 * from a TemporalAccessor or empty if it doesn't contain a year.
+	 *
+	 * @param theTemporalAccessor The TemporalAccessor containing date/time information
+	 * @return A LocalDateTime or empty
+	 */
+	public static Optional<LocalDateTime> extractLocalDateTimeForRangeEndOrEmpty(TemporalAccessor theTemporalAccessor) {
+		if (theTemporalAccessor.isSupported(ChronoField.YEAR)) {
+			final int year = theTemporalAccessor.get(ChronoField.YEAR);
+			final Month month = Month.of(getTimeUnitIfSupported(theTemporalAccessor, ChronoField.MONTH_OF_YEAR, 12));
+			final int day = getTimeUnitIfSupported(
+					theTemporalAccessor,
+					ChronoField.DAY_OF_MONTH,
+					YearMonth.of(year, month).atEndOfMonth().getDayOfMonth());
+			final int hour = getTimeUnitIfSupported(theTemporalAccessor, ChronoField.HOUR_OF_DAY, 23);
+			final int minute = getTimeUnitIfSupported(theTemporalAccessor, ChronoField.MINUTE_OF_HOUR, 59);
+			final int seconds = getTimeUnitIfSupported(theTemporalAccessor, ChronoField.SECOND_OF_MINUTE, 59);
+
+			return Optional.of(LocalDateTime.of(year, month, day, hour, minute, seconds));
+		}
+
+		return Optional.empty();
+	}
+
+	/**
+	 * With the provided DateTimeFormatter, parse a date time String or return empty if the String doesn't correspond
+	 * to the formatter.
+	 *
+	 * @param theDateTimeString A date/time String in some date format
+	 * @param theSupportedDateTimeFormatter The DateTimeFormatter we expect corresponds to the String
+	 * @return The parsed TemporalAccessor or empty
+	 */
+	public static Optional<TemporalAccessor> parseDateTimeStringIfValid(
+			String theDateTimeString, DateTimeFormatter theSupportedDateTimeFormatter) {
+		Objects.requireNonNull(theSupportedDateTimeFormatter);
+		Preconditions.checkArgument(StringUtils.isNotBlank(theDateTimeString));
+
+		try {
+			return Optional.of(theSupportedDateTimeFormatter.parse(theDateTimeString));
+		} catch (Exception exception) {
+			return Optional.empty();
+		}
+	}
+
+	private static int getTimeUnitIfSupported(
+			TemporalAccessor theTemporalAccessor, TemporalField theTemporalField, int theDefaultValue) {
+		return getTimeUnitIfSupportedOrEmpty(theTemporalAccessor, theTemporalField)
+				.orElse(theDefaultValue);
+	}
+
+	private static Optional<Integer> getTimeUnitIfSupportedOrEmpty(
+			TemporalAccessor theTemporalAccessor, TemporalField theTemporalField) {
+		if (theTemporalAccessor.isSupported(theTemporalField)) {
+			return Optional.of(theTemporalAccessor.get(theTemporalField));
+		}
+
+		return Optional.empty();
+	}
+
 	/**
 	 * A factory for {@link SimpleDateFormat}s. The instances are stored in a
 	 * threadlocal way because SimpleDateFormat is not thread safe as noted in

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

@@ -110,6 +110,12 @@ public class HapiExtensions {
 
 	public static final String EXT_SP_UNIQUE = "http://hapifhir.io/fhir/StructureDefinition/sp-unique";
 
+	/**
+	 * URL for extension on a Search Parameter which determines whether it should be enabled for searching for resources
+	 */
+	public static final String EXT_SEARCHPARAM_ENABLED_FOR_SEARCHING =
+			"http://hapifhir.io/fhir/StructureDefinition/searchparameter-enabled-for-searching";
+
 	/**
 	 * URL for extension on a Phonetic String SearchParameter indicating that text values should be phonetically indexed with the named encoder
 	 */

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

@@ -34,6 +34,7 @@ import com.fasterxml.jackson.databind.ser.FilterProvider;
 import com.fasterxml.jackson.databind.ser.PropertyWriter;
 import com.fasterxml.jackson.databind.ser.impl.SimpleBeanPropertyFilter;
 import com.fasterxml.jackson.databind.ser.impl.SimpleFilterProvider;
+import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
 import jakarta.annotation.Nonnull;
 
 import java.io.IOException;
@@ -60,16 +61,22 @@ public class JsonUtil {
 		ourMapperPrettyPrint.setSerializationInclusion(JsonInclude.Include.NON_NULL);
 		ourMapperPrettyPrint.setFilterProvider(SENSITIVE_DATA_FILTER_PROVIDER);
 		ourMapperPrettyPrint.enable(SerializationFeature.INDENT_OUTPUT);
+		// Needed to handle ZonedDateTime
+		ourMapperPrettyPrint.registerModule(new JavaTimeModule());
 
 		ourMapperNonPrettyPrint = new ObjectMapper();
 		ourMapperNonPrettyPrint.setSerializationInclusion(JsonInclude.Include.NON_NULL);
 		ourMapperNonPrettyPrint.setFilterProvider(SENSITIVE_DATA_FILTER_PROVIDER);
 		ourMapperNonPrettyPrint.disable(SerializationFeature.INDENT_OUTPUT);
+		// Needed to handle ZonedDateTime
+		ourMapperNonPrettyPrint.registerModule(new JavaTimeModule());
 
 		ourMapperIncludeSensitive = new ObjectMapper();
 		ourMapperIncludeSensitive.setFilterProvider(SHOW_ALL_DATA_FILTER_PROVIDER);
 		ourMapperIncludeSensitive.setSerializationInclusion(JsonInclude.Include.NON_NULL);
 		ourMapperIncludeSensitive.disable(SerializationFeature.INDENT_OUTPUT);
+		// Needed to handle ZonedDateTime
+		ourMapperIncludeSensitive.registerModule(new JavaTimeModule());
 	}
 
 	/**

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

@@ -43,6 +43,7 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.List;
+import java.util.Objects;
 import java.util.Optional;
 import java.util.function.Function;
 import java.util.stream.Collectors;
@@ -58,20 +59,20 @@ public class ParametersUtil {
 	public static Optional<String> getNamedParameterValueAsString(
 			FhirContext theCtx, IBaseParameters theParameters, String theParameterName) {
 		Function<IPrimitiveType<?>, String> mapper = t -> defaultIfBlank(t.getValueAsString(), null);
-		return extractNamedParameters(theCtx, theParameters, theParameterName, mapper).stream()
+		return extractNamedParameterValues(theCtx, theParameters, theParameterName, mapper).stream()
 				.findFirst();
 	}
 
 	public static List<String> getNamedParameterValuesAsString(
 			FhirContext theCtx, IBaseParameters theParameters, String theParameterName) {
 		Function<IPrimitiveType<?>, String> mapper = t -> defaultIfBlank(t.getValueAsString(), null);
-		return extractNamedParameters(theCtx, theParameters, theParameterName, mapper);
+		return extractNamedParameterValues(theCtx, theParameters, theParameterName, mapper);
 	}
 
 	public static List<Integer> getNamedParameterValuesAsInteger(
 			FhirContext theCtx, IBaseParameters theParameters, String theParameterName) {
 		Function<IPrimitiveType<?>, Integer> mapper = t -> (Integer) t.getValue();
-		return extractNamedParameters(theCtx, theParameters, theParameterName, mapper);
+		return extractNamedParameterValues(theCtx, theParameters, theParameterName, mapper);
 	}
 
 	public static Optional<Integer> getNamedParameterValueAsInteger(
@@ -80,6 +81,19 @@ public class ParametersUtil {
 				.findFirst();
 	}
 
+	/**
+	 * Returns the resource within a parameter.
+	 * @param theCtx thr FHIR context
+	 * @param theParameters the parameters instance where to look for the resource
+	 * @param theParameterName the parameter name
+	 * @return the resource
+	 */
+	public static Optional<IBaseResource> getNamedParameterResource(
+			FhirContext theCtx, IBaseParameters theParameters, String theParameterName) {
+		return extractNamedParameterResources(theCtx, theParameters, theParameterName).stream()
+				.findFirst();
+	}
+
 	public static Optional<IBase> getNamedParameter(
 			FhirContext theCtx, IBaseResource theParameters, String theParameterName) {
 		return getNamedParameters(theCtx, theParameters, theParameterName).stream()
@@ -153,7 +167,7 @@ public class ParametersUtil {
 				.map(t -> (Integer) t);
 	}
 
-	private static <T> List<T> extractNamedParameters(
+	private static <T> List<T> extractNamedParameterValues(
 			FhirContext theCtx,
 			IBaseParameters theParameters,
 			String theParameterName,
@@ -170,7 +184,25 @@ public class ParametersUtil {
 					.filter(t -> t instanceof IPrimitiveType<?>)
 					.map(t -> ((IPrimitiveType<?>) t))
 					.map(theMapper)
-					.filter(t -> t != null)
+					.filter(Objects::nonNull)
+					.forEach(retVal::add);
+		}
+		return retVal;
+	}
+
+	private static List<IBaseResource> extractNamedParameterResources(
+			FhirContext theCtx, IBaseParameters theParameters, String theParameterName) {
+		List<IBaseResource> retVal = new ArrayList<>();
+
+		List<IBase> namedParameters = getNamedParameters(theCtx, theParameters, theParameterName);
+		for (IBase nextParameter : namedParameters) {
+			BaseRuntimeElementCompositeDefinition<?> nextParameterDef =
+					(BaseRuntimeElementCompositeDefinition<?>) theCtx.getElementDefinition(nextParameter.getClass());
+			BaseRuntimeChildDefinition resourceChild = nextParameterDef.getChildByName("resource");
+			List<IBase> resourceValues = resourceChild.getAccessor().getValues(nextParameter);
+			resourceValues.stream()
+					.filter(IBaseResource.class::isInstance)
+					.map(t -> ((IBaseResource) t))
 					.forEach(retVal::add);
 		}
 		return retVal;

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

@@ -26,10 +26,12 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeChildChoiceDefinition;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.i18n.Msg;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.tuple.Triple;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
+import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.slf4j.Logger;
@@ -93,6 +95,8 @@ public final class TerserUtil {
 
 	private static final Logger ourLog = getLogger(TerserUtil.class);
 	private static final String EQUALS_DEEP = "equalsDeep";
+	public static final String DATA_ABSENT_REASON_EXTENSION_URI =
+			"http://hl7.org/fhir/StructureDefinition/data-absent-reason";
 
 	private TerserUtil() {}
 
@@ -266,6 +270,15 @@ public final class TerserUtil {
 		return theItems.stream().anyMatch(i -> equals(i, theItem, method));
 	}
 
+	private static boolean hasDataAbsentReason(IBase theItem) {
+		if (theItem instanceof IBaseHasExtensions) {
+			IBaseHasExtensions hasExtensions = (IBaseHasExtensions) theItem;
+			return hasExtensions.getExtension().stream()
+					.anyMatch(t -> StringUtils.equals(t.getUrl(), DATA_ABSENT_REASON_EXTENSION_URI));
+		}
+		return false;
+	}
+
 	/**
 	 * Merges all fields on the provided instance. <code>theTo</code> will contain a union of all values from <code>theFrom</code>
 	 * instance and <code>theTo</code> instance.
@@ -695,24 +708,36 @@ public final class TerserUtil {
 			BaseRuntimeChildDefinition childDefinition,
 			List<IBase> theFromFieldValues,
 			List<IBase> theToFieldValues) {
-		for (IBase theFromFieldValue : theFromFieldValues) {
+		if (!theFromFieldValues.isEmpty() && theToFieldValues.stream().anyMatch(TerserUtil::hasDataAbsentReason)) {
-			if (contains(theFromFieldValue, theToFieldValues)) {
+			// If the to resource has a data absent reason, and there is potentially real data incoming
+			// in the from resource, we should clear the data absent reason because it won't be absent anymore.
+			theToFieldValues = removeDataAbsentReason(theTo, childDefinition, theToFieldValues);
+		}
+
+		for (IBase fromFieldValue : theFromFieldValues) {
+			if (contains(fromFieldValue, theToFieldValues)) {
 				continue;
 			}
 
-			IBase newFieldValue = newElement(theTerser, childDefinition, theFromFieldValue, null);
+			if (hasDataAbsentReason(fromFieldValue) && !theToFieldValues.isEmpty()) {
-			if (theFromFieldValue instanceof IPrimitiveType) {
+				// if the from field value asserts a reason the field isn't populated, but the to field is populated,
+				// we don't want to overwrite real data with the extension
+				continue;
+			}
+
+			IBase newFieldValue = newElement(theTerser, childDefinition, fromFieldValue, null);
+			if (fromFieldValue instanceof IPrimitiveType) {
 				try {
-					Method copyMethod = getMethod(theFromFieldValue, "copy");
+					Method copyMethod = getMethod(fromFieldValue, "copy");
 					if (copyMethod != null) {
-						newFieldValue = (IBase) copyMethod.invoke(theFromFieldValue, new Object[] {});
+						newFieldValue = (IBase) copyMethod.invoke(fromFieldValue, new Object[] {});
 					}
 				} catch (Throwable t) {
-					((IPrimitiveType) newFieldValue)
+					((IPrimitiveType<?>) newFieldValue)
-							.setValueAsString(((IPrimitiveType) theFromFieldValue).getValueAsString());
+							.setValueAsString(((IPrimitiveType<?>) fromFieldValue).getValueAsString());
 				}
 			} else {
-				theTerser.cloneInto(theFromFieldValue, newFieldValue, true);
+				theTerser.cloneInto(fromFieldValue, newFieldValue, true);
 			}
 
 			try {
@@ -724,6 +749,21 @@ public final class TerserUtil {
 		}
 	}
 
+	private static List<IBase> removeDataAbsentReason(
+			IBaseResource theResource, BaseRuntimeChildDefinition theFieldDefinition, List<IBase> theFieldValues) {
+		for (int i = 0; i < theFieldValues.size(); i++) {
+			if (hasDataAbsentReason(theFieldValues.get(i))) {
+				try {
+					theFieldDefinition.getMutator().remove(theResource, i);
+				} catch (UnsupportedOperationException e) {
+					// the field must be single-valued, just clear it
+					theFieldDefinition.getMutator().setValue(theResource, null);
+				}
+			}
+		}
+		return theFieldDefinition.getAccessor().getValues(theResource);
+	}
+
 	/**
 	 * Clones the specified resource.
 	 *

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

@@ -162,9 +162,16 @@ public enum VersionEnum {
 
 	V7_3_0,
 	V7_4_0,
+	V7_4_1,
+	V7_4_2,
+	V7_4_3,
+	V7_4_4,
+	V7_4_5,
 
 	V7_5_0,
-	V7_6_0;
+	V7_6_0,
+	V7_7_0,
+	V7_8_0;
 
 	public static VersionEnum latestVersion() {
 		VersionEnum[] values = VersionEnum.values();

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

@@ -133,6 +133,7 @@ ca.uhn.fhir.jpa.dao.BaseStorageDao.successfulTimingSuffix=Took {0}ms.
 ca.uhn.fhir.jpa.dao.BaseStorageDao.deleteResourceNotExisting=Not deleted, resource {0} does not exist.
 ca.uhn.fhir.jpa.dao.BaseStorageDao.deleteResourceAlreadyDeleted=Not deleted, resource {0} was already deleted.
 ca.uhn.fhir.jpa.dao.BaseStorageDao.invalidSearchParameter=Unknown search parameter "{0}" for resource type "{1}". Valid search parameters for this search are: {2}
+ca.uhn.fhir.jpa.dao.BaseStorageDao.invalidSearchParameterNotEnabledForSearch=Search parameter "{0}" for resource type "{1}" is not active for searching. Valid search parameters for this search are: {2}
 ca.uhn.fhir.jpa.dao.BaseStorageDao.invalidSortParameter=Unknown _sort parameter value "{0}" for resource type "{1}" (Note: sort parameters values must use a valid Search Parameter). Valid values for this search are: {2}
 ca.uhn.fhir.jpa.dao.BaseStorageDao.invalidSortParameterTooManyChains=Invalid _sort expression, can not chain more than once in a sort expression: {0}
 

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

@@ -0,0 +1,179 @@
+package ca.uhn.fhir.util;
+
+import jakarta.annotation.Nullable;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.MethodSource;
+
+import java.time.LocalDateTime;
+import java.time.Month;
+import java.time.format.DateTimeFormatter;
+import java.time.temporal.TemporalAccessor;
+import java.util.Optional;
+import java.util.stream.Stream;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+class DateUtilsTest {
+
+	private static final DateTimeFormatter DATE_TIME_FORMATTER_YYYY = DateTimeFormatter.ofPattern("yyyy");
+	private static final DateTimeFormatter DATE_TIME_FORMATTER_YYYY_MM = DateTimeFormatter.ofPattern("yyyy-MM");
+	private static final DateTimeFormatter DATE_TIME_FORMATTER_YYYY_MM_DD = DateTimeFormatter.ISO_DATE;
+	private static final DateTimeFormatter DATE_TIME_FORMATTER_YYYY_MM_DD_HH = DateTimeFormatter.ofPattern("yyyy-MM-dd'T'HH");
+	private static final DateTimeFormatter DATE_TIME_FORMATTER_YYYY_MM_DD_HH_MM = DateTimeFormatter.ofPattern("yyyy-MM-dd'T'HH:mm");
+	private static final DateTimeFormatter DATE_TIME_FORMATTER_YYYY_MM_DD_HH_MM_SS = DateTimeFormatter.ISO_LOCAL_DATE_TIME;
+
+	private static Stream<Arguments> extractLocalDateTimeStartIfValidParams() {
+		return Stream.of(
+			Arguments.of(
+				getTemporalAccessor("2024"),
+				LocalDateTime.of(2024, Month.JANUARY, 1, 0, 0, 0)
+			),
+			Arguments.of(
+				getTemporalAccessor("2023-02"),
+				LocalDateTime.of(2023, Month.FEBRUARY, 1, 0, 0, 0)
+			),
+			Arguments.of(
+				getTemporalAccessor("2022-09"),
+				LocalDateTime.of(2022, Month.SEPTEMBER, 1, 0, 0, 0)
+			),
+			Arguments.of(
+				getTemporalAccessor("2021-03-24"),
+				LocalDateTime.of(2021, Month.MARCH, 24, 0, 0, 0)
+			),
+			Arguments.of(
+				getTemporalAccessor("2024-10-23"),
+				LocalDateTime.of(2024, Month.OCTOBER, 23, 0, 0, 0)
+			),
+			Arguments.of(
+				getTemporalAccessor("2024-08-24T12"),
+				LocalDateTime.of(2024, Month.AUGUST, 24, 12, 0, 0)
+			),
+			Arguments.of(
+				getTemporalAccessor("2024-11-24T12:35"),
+				LocalDateTime.of(2024, Month.NOVEMBER, 24, 12, 35, 0)
+			),
+			Arguments.of(
+				getTemporalAccessor("2024-09-24T12:35:47"),
+				LocalDateTime.of(2024, Month.SEPTEMBER, 24, 12, 35, 47)
+			)
+		);
+	}
+
+	private static Stream<Arguments> extractLocalDateTimeEndIfValidParams() {
+		return Stream.of(
+			Arguments.of(
+				getTemporalAccessor("2024"),
+				LocalDateTime.of(2024, Month.DECEMBER, 31, 23, 59, 59)
+			),
+			Arguments.of(
+				getTemporalAccessor("2023-01"),
+				LocalDateTime.of(2023, Month.JANUARY, 31, 23, 59, 59)
+			),
+			Arguments.of(
+				getTemporalAccessor("2023-02"),
+				LocalDateTime.of(2023, Month.FEBRUARY, 28, 23, 59, 59)
+			),
+			// Leap year
+			Arguments.of(
+				getTemporalAccessor("2024-02"),
+				LocalDateTime.of(2024, Month.FEBRUARY, 29, 23, 59, 59)
+			),
+			Arguments.of(
+				getTemporalAccessor("2023-03"),
+				LocalDateTime.of(2023, Month.MARCH, 31, 23, 59, 59)
+			),
+			Arguments.of(
+				getTemporalAccessor("2023-04"),
+				LocalDateTime.of(2023, Month.APRIL, 30, 23, 59, 59)
+			),
+			Arguments.of(
+				getTemporalAccessor("2023-05"),
+				LocalDateTime.of(2023, Month.MAY, 31, 23, 59, 59)
+			),
+			Arguments.of(
+				getTemporalAccessor("2023-06"),
+				LocalDateTime.of(2023, Month.JUNE, 30, 23, 59, 59)
+			),
+			Arguments.of(
+				getTemporalAccessor("2023-07"),
+				LocalDateTime.of(2023, Month.JULY, 31, 23, 59, 59)
+			),
+			Arguments.of(
+				getTemporalAccessor("2023-08"),
+				LocalDateTime.of(2023, Month.AUGUST, 31, 23, 59, 59)
+			),
+			Arguments.of(
+				getTemporalAccessor("2023-09"),
+				LocalDateTime.of(2023, Month.SEPTEMBER, 30, 23, 59, 59)
+			),
+			Arguments.of(
+				getTemporalAccessor("2022-10"),
+				LocalDateTime.of(2022, Month.OCTOBER, 31, 23, 59, 59)
+			),
+			Arguments.of(
+				getTemporalAccessor("2022-11"),
+				LocalDateTime.of(2022, Month.NOVEMBER, 30, 23, 59, 59)
+			),
+			Arguments.of(
+				getTemporalAccessor("2022-12"),
+				LocalDateTime.of(2022, Month.DECEMBER, 31, 23, 59, 59)
+			),
+			Arguments.of(
+				getTemporalAccessor("2021-03-24"),
+				LocalDateTime.of(2021, Month.MARCH, 24, 23, 59, 59)
+			),
+			Arguments.of(
+				getTemporalAccessor("2024-10-23"),
+				LocalDateTime.of(2024, Month.OCTOBER, 23, 23, 59, 59)
+			),
+			Arguments.of(
+				getTemporalAccessor("2024-09-24T12:35:47"),
+				LocalDateTime.of(2024, Month.SEPTEMBER, 24, 12, 35, 47)
+			)
+		);
+	}
+
+	@ParameterizedTest
+	@MethodSource("extractLocalDateTimeStartIfValidParams")
+	void extractLocalDateTimeStartIfValid (
+			TemporalAccessor theTemporalAccessor,
+			@Nullable LocalDateTime theExpectedResult) {
+		assertThat(DateUtils.extractLocalDateTimeForRangeStartOrEmpty(theTemporalAccessor))
+			.isEqualTo(Optional.ofNullable(theExpectedResult));
+	}
+
+	@ParameterizedTest
+	@MethodSource("extractLocalDateTimeEndIfValidParams")
+	void extractLocalDateTimeEndIfValid (
+		TemporalAccessor theTemporalAccessor,
+		@Nullable LocalDateTime theExpectedResult) {
+		assertThat(DateUtils.extractLocalDateTimeForRangeEndOrEmpty(theTemporalAccessor))
+			.isEqualTo(Optional.ofNullable(theExpectedResult));
+	}
+
+	private static TemporalAccessor getTemporalAccessor(String theDateTimeString) {
+		final DateTimeFormatter dateTimeFormatter = getDateTimeFormatter(theDateTimeString);
+
+		assertThat(dateTimeFormatter)
+			.withFailMessage("Cannot find DateTimeFormatter for: " + theDateTimeString)
+			.isNotNull();
+
+		return DateUtils.parseDateTimeStringIfValid(
+			theDateTimeString,
+			dateTimeFormatter
+		).orElseThrow(() -> new IllegalArgumentException("Unable to parse: " + theDateTimeString));
+	}
+
+	private static DateTimeFormatter getDateTimeFormatter(String theDateTimeString) {
+		return switch (theDateTimeString.length()) {
+			case 4 -> DATE_TIME_FORMATTER_YYYY;
+			case 7 -> DATE_TIME_FORMATTER_YYYY_MM;
+			case 10 -> DATE_TIME_FORMATTER_YYYY_MM_DD;
+			case 13 -> DATE_TIME_FORMATTER_YYYY_MM_DD_HH;
+			case 16 -> DATE_TIME_FORMATTER_YYYY_MM_DD_HH_MM;
+			case 19 -> DATE_TIME_FORMATTER_YYYY_MM_DD_HH_MM_SS;
+			default -> null;
+		};
+	}
+}

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

@@ -77,5 +77,4 @@ public class TaskChunkerTest {
 			Arguments.of(List.of(1,2,3,4,5,6,7,8,9), List.of(List.of(1,2,3), List.of(4,5,6), List.of(7,8,9)))
 		);
 	}
-
 }

hapi-fhir-bom/pom.xml

@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>ca.uhn.hapi.fhir</groupId>
 	<artifactId>hapi-fhir-bom</artifactId>
-	<version>7.5.1-SNAPSHOT</version>
+	<version>7.7.3-SNAPSHOT</version>
 
 	<packaging>pom</packaging>
 	<name>HAPI FHIR BOM</name>
@@ -12,7 +12,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.1-SNAPSHOT</version>
+		<version>7.7.3-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>7.5.1-SNAPSHOT</version>
+		<version>7.7.3-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-checkstyle/src/checkstyle/hapi-base-checkstyle.xml

@@ -64,4 +64,12 @@
 			<property name="format" value="^(Base|Abstract).+$"/>
 		</module>
 	</module>
+
+	<!-- for suppression of rules; to use, surround code to exclude with comments: -->
+	<!-- CHECKSTYLE.OFF RuleToDisable   AND   CHECKSTYLE.ON RuleToDisable -->
+	<module name="SuppressWithPlainTextCommentFilter">
+		<property name="offCommentFormat" value="CHECKSTYLE.OFF\: ([\w\|]+)" />
+		<property name="onCommentFormat" value="CHECKSTYLE.ON\: ([\w\|]+)" />
+	</module>
+
 </module>

hapi-fhir-cli/hapi-fhir-cli-api/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.1-SNAPSHOT</version>
+		<version>7.7.3-SNAPSHOT</version>
 
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-cli/hapi-fhir-cli-app/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-cli</artifactId>
-		<version>7.5.1-SNAPSHOT</version>
+		<version>7.7.3-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-cli/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>7.5.1-SNAPSHOT</version>
+		<version>7.7.3-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-client-okhttp/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.1-SNAPSHOT</version>
+		<version>7.7.3-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-client-okhttp/src/test/java/ca/uhn/fhir/okhttp/GenericOkHttpClientDstu2Test.java

@@ -1357,7 +1357,9 @@ public class GenericOkHttpClientDstu2Test {
 			.returnBundle(Bundle.class)
 			.execute();
 
-		assertEquals(ourServer.getBaseUrl() + "/fhir/Patient/_search?_elements=identifier%2Cname", MY_SERVLET.ourRequestUri);
+		assertThat(MY_SERVLET.ourRequestUri).isIn(
+			ourServer.getBaseUrl() + "/fhir/Patient/_search?_elements=identifier%2Cname",
+			ourServer.getBaseUrl() + "/fhir/Patient/_search?_elements=name%2Cidentifier");
 
 		// assertThat(MY_SERVLET.ourRequestUri,
 		// either(equalTo(ourServer.getBaseUrl() + "/fhir/Patient?name=james&_elements=name%2Cidentifier")).or(equalTo(ourServer.getBaseUrl() +
@@ -1391,7 +1393,10 @@ public class GenericOkHttpClientDstu2Test {
 			.execute();
 
 		assertThat(MY_SERVLET.ourRequestUri).contains(ourServer.getBaseUrl() + "/fhir/Patient/_search?");
-		assertThat(MY_SERVLET.ourRequestUri).contains("_elements=identifier%2Cname");
+		assertThat(MY_SERVLET.ourRequestUri).satisfiesAnyOf(
+			s -> assertThat(s).contains("_elements=identifier%2Cname"),
+			s -> assertThat(s).contains("_elements=name%2Cidentifier")
+		);
 		assertThat(MY_SERVLET.ourRequestUri).doesNotContain("_format=json");
 
 		// assertThat(MY_SERVLET.ourRequestUri,

hapi-fhir-client/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.1-SNAPSHOT</version>
+		<version>7.7.3-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-converter/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.1-SNAPSHOT</version>
+		<version>7.7.3-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-dist/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>7.5.1-SNAPSHOT</version>
+		<version>7.7.3-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-docs/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.1-SNAPSHOT</version>
+		<version>7.7.3-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/BundleFetcher.java

@@ -39,7 +39,7 @@ public class BundleFetcher {
 		// START SNIPPET: loadAll
 		// Create a context and a client
 		FhirContext ctx = FhirContext.forR4();
-		String serverBase = "http://hapi.fhr.org/baseR4";
+		String serverBase = "http://hapi.fhir.org/baseR4";
 		IGenericClient client = ctx.newRestfulGenericClient(serverBase);
 
 		// We'll populate this list

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/version.yaml

@@ -1,3 +1,3 @@
 ---
-release-date: "2023-02-18"
+release-date: "2024-02-18"
 codename: "Apollo"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/version.yaml

@@ -1,3 +1,3 @@
 ---
-release-date: "2023-05-18"
+release-date: "2024-05-18"
 codename: "Borealis"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_2/version.yaml

@@ -0,0 +1,3 @@
+---
+release-date: "2024-09-20"
+codename: "Copernicus"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_3/version.yaml

@@ -0,0 +1,3 @@
+---
+release-date: "2024-09-30"
+codename: "Copernicus"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_4/6363-updating-fhir-core-dependency.yaml

@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 6363
+title: "This release updates the org.hl7.fhir core dependency up to 6.3.23, in order to patch [CVE-2024-45294](https://nvd.nist.gov/vuln/detail/CVE-2024-45294)."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_4/version.yaml

@@ -0,0 +1,3 @@
+---
+release-date: "2024-10-17"
+codename: "Copernicus"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_5/version.yaml

@@ -0,0 +1,3 @@
+---
+release-date: "2024-10-21"
+codename: "Copernicus"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6210-add-chunk-id-to-delete-expunge-log-msg.yaml

@@ -0,0 +1,6 @@
+---
+type: add
+issue: 6210
+jira: SMILE-8428
+title: "Batch instance ID and chunk ID have been added to the logging context so that they can be automatically added to
+batch-related messages in the log."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6216-fulltext-searching-not-returning-expected-results.yaml

@@ -1,6 +1,6 @@
 ---
 type: fix
-backport: 7.2.3
+backport: 7.2.3,7.4.2
 issue: 6216
 jira: SMILE-8806
 title: "Previously, searches combining the `_text` query parameter (using Lucene/Elasticsearch) with query parameters 

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6252-improve-validator-performance.yaml

@@ -0,0 +1,6 @@
+---
+type: perf
+issue: 6253
+title: "A cache has been added to the validation services layer which results
+  in improved validation performance. Thanks to Max Bureck for the
+  contribution!"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6285-batch2-reindex-version2-added.yaml

@@ -0,0 +1,17 @@
+---
+type: fix
+issue: 6285
+title: "Updated the Reindex Batch2 job to allow
+        for an additional step that will check to ensure
+        that no pending 'reindex' work is needed.
+        This was done to prevent a bug in which
+        value set expansion would not return all
+        the existing CodeSystem Concepts after
+        a reindex call, due to some of the concepts
+        being deferred to future job runs.
+        
+        As such, `$reindex` operations on CodeSystems
+        will no longer result in incorrect value set
+        expansion when such an expansion is called
+        'too soon' after a $reindex operation.
+"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6313-add-pointcut-for-delete-partition.yaml

@@ -0,0 +1,6 @@
+---
+type: add
+issue: 6313
+jira: SMILE-8847
+title: "The `STORAGE_PARTITION_DELETED` pointcut has been added and will be called upon deleting a partition 
+using the `$partition-management-delete-partition` operation."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6317-fix-resource-duplication-for-composite-unique-sp-with-date-time-component.yaml

@@ -1,6 +1,7 @@
 ---
 type: fix
 issue: 6317
+backport: 7.4.3
 title: "Previously, defining a unique combo Search Parameter with the DateTime component and submitting multiple 
 resources with the same dateTime element (e.g. Observation.effectiveDateTime) resulted in duplicate resource creation. 
 This has been fixed."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6323-concurrent-constructor-access.yaml

@@ -0,0 +1,5 @@
+---
+type: perf
+issue: 6323
+title: "A synchronization choke point was removed from the model object initialization code, reducing the risk of
+multi-thread contention."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6325-partitioned-search.yaml

@@ -0,0 +1,5 @@
+---
+type: add
+issue: 6325
+title: "A new configuration option, `PartitionSettings#setPartitionIdsInPrimaryKeys(boolean)` configures the query engine
+   to include the partitioning column in search query joins."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6339-drop-index-nondefault-schema.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 6339
+jira: SMILE-9044
+title: "Fixed a bug in migrations when using Postgres when using the non-default schema. If a migration attempted to drop a primary key, the generated SQL would only ever target the `public` schema.
+This has been corrected, and the current schema is now used, with `public` as a fallback. Thanks to Adrienne Sox for the contribution!"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6341-expand-translation-cache.yaml

@@ -0,0 +1,6 @@
+---
+type: change
+issue: 6341
+title: "The CachingValidationSupport cache for concept translations will 
+   now keep up to 500000 translations instead of the previous 5000. 
+   This will be made configurable in a future release."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6345-date-searching-performance-tweaking.yaml

@@ -0,0 +1,8 @@
+---
+type: perf
+issue: 6345
+title: "Date searches using equality would perform badly as the query planner
+        does not know that our LOW_VALUE columns are always < HIGH_VALUE
+        columns, and HIGH_VALUE is always > LOW_VALUE columns.
+        These queries have been fixed to account for this.
+"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6357-update-cr-version.yaml

@@ -0,0 +1,6 @@
+---
+type: add
+issue: 6357
+title: Upgrade the Clinical Reasoning module to the latest release of 3.13.0. This update comes with several changes
+    and feature enhancements to CPG and dQM clinical-reasoning operations. Please review associated ticket and upgrade.md
+    for detailed list of changes.

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6359-remote-terminology-validation-does-not-error-for-invalid-codes.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 6359
+backport: 7.4.4
+title: "After upgrading org.hl7.fhir.core from 6.1.2.2 to 6.3.11, the $validate-code operation stopped returning an 
+error for invalid codes using remote terminology. This has been fixed."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6359-support-for-out-parameter-issues-remote-terminology-validation.yaml

@@ -0,0 +1,6 @@
+---
+type: add
+issue: 6359
+backport: 7.4.4
+title: "Remote Terminology validation has been enhanced to support output parameter `issues` for the $validate-code 
+operation."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6365-fix-include-crash-on-mssql.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 6365
+title: "A crash while executing a search with named `_include` parameters on
+  MSSQL has been fixed. Thanks to Craig McClendon for the pull request!"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6366-consent-plumbing.yaml

@@ -0,0 +1,4 @@
+---
+type: add
+issue: 6366
+title: "Add plumbing for combining IConsentServices with different vote tally strategies"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6370-data-absent-merge.yaml

@@ -0,0 +1,6 @@
+---
+type: add
+issue: 6370
+title: "When using the FHIR `TerserUtil` to merge two resource, if one resource has real data in a particular field,
+and the other resource has a `data-absent-reason` extension in the same field, the real data will be given
+precedence in the merged resource, and the extension will be ignored."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6372-lucene-and-jpa-search-combine-issues.yaml

@@ -0,0 +1,10 @@
+---
+type: fix
+issue: 6372
+jira: SMILE-9073
+backport: 7.4.5
+title: "Searches that combined full-text searching (i.e. `_text` or `_content`)
+    with other search parameters could fail to return all results if we encountered
+    1600 matches against the full-text index where none of them match the rest of the query.
+    This has now been fixed.
+"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6375-add-hash-identity-token-mode.yaml

@@ -0,0 +1,6 @@
+---
+type: add
+issue: 6375
+title: "A new experimental JPA setting has been added to JpaStorageSettings which
+  causes searches for token SearchParameters to include a predicate on the
+  HASH_IDENTITY column even if it is not needed because other hashes are in use."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/changes.yaml

@@ -4,7 +4,7 @@
       title: "The version of a few dependencies have been bumped to more recent versions
       (dependent HAPI modules listed in brackets):
       <ul>
-      <li>org.hl7.fhir.core (Base): 6.3.18 -&gt; 6.3.23</li>
+      <li>org.hl7.fhir.core (Base): 6.3.18 -&gt; 6.3.25</li>
       <li>Bower/Moment.js (hapi-fhir-testpage-overlay): 2.27.0 -&gt; 2.29.4</li>
       <li>htmlunit (Base): 3.9.0 -&gt; 3.11.0</li>
       <li>Elasticsearch (Base): 8.11.1 -&gt; 8.14.3</li>

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/upgrade.md

@@ -0,0 +1,25 @@
+# Measures and Care Gaps
+
+## TimeZone Header 
+DQM `$care-gaps` and `$evaluate-measure`  will convert parameters `periodStart` and `periodEnd`
+according to a timezone supplied by the client, not the server timezone as it was previously.  Clients can leverage this
+functionality by passing in a new `Timezone` header (ex: `America/Denver`).  If nothing is supplied, it will default to
+UTC.
+
+## CareGaps Operation Parameters
+### Parameters removed
+Certain `$care-gaps` operation parameters have been dropped, because they are not used or likely to be implemented
+* `topic`
+* `practitioner` is now callable via `subject` parameter
+* `organization`
+* `program`
+
+### Parameters added:
+* `measureIdentifier` now is available to resolve measure resources for evaluation
+* `nonDocument` is a new optional parameter that defaults to `false` which returns standard `document` bundle for `$care-gaps`. 
+If `true`, this will return summarized subject bundle with only detectedIssue.
+
+# SDC $populate operation
+
+The `subject` parameter of the `Questionnaire/$populate` operation has been changed to expect a `Reference` as specified
+in the SDC IG. 

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6107-allow-sp-disabling.yaml

@@ -0,0 +1,7 @@
+---
+type: add
+issue: 6107
+title: "A new extension has been created for use on SearchParameter resources in the JPA server. This extension causes
+   a SearchParameter to be indexed, but to not be available for use in searches. This can be set when a new SP is created
+   in order to prevent it from being used before an index has been completed. See
+   [Introducing Search Parameters on Existing Data](https://smilecdr.com/docs/fhir_standard/fhir_search_custom_search_parameters.html) for more information."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6224-resolve-tag-definition-in-same-thread.yaml

@@ -0,0 +1,7 @@
+---
+type: perf
+issue: 6224
+title: "The JPA server will no longer use a separate thread and database connection
+  to resolve tag definitions. This should improve performance in some cases, and
+  resolves compatibility issues for some environments. Thanks to Ibrahim (Trifork A/S)
+  for the pull request!"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6258-improve-auth-interceptor-operation-handling.yaml

@@ -0,0 +1,10 @@
+---
+type: fix
+issue: 6258
+title: "The AuthorizationInterceptor handling for operations has been improved
+  so that operation rules now directly test the contents of response Bundle
+  or Parameters objects returned by the operation when configure to require
+  explicit response authorization. This fixes a regression in 7.4.0 where
+  operation responses could sometimes be denied even if appropriate
+  permissions were granted to view resources in a response bundle. Thanks to
+  Gijsbert van den Brink for reporting the issue with a sample test!"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6395-allow-submit-subscription-synchronously.yaml

@@ -0,0 +1,7 @@
+---
+type: perf
+issue: 6395
+title: "A new configuration option has been added to `SubsciptionSubmitterConfig` which
+  causes Subscription resources to be submitted to the processing queue synchronously
+  instead of asynchronously as all other resources are. This is useful for cases where
+  subscriptions need to be activated quickly. Thanks to Michal Sevcik for the contribution!"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6398-add-author-search-to-npm-search.yaml

@@ -0,0 +1,5 @@
+---
+type: add
+issue: 6398
+title: "The NPM package search module has been enhanced to support searching by
+  the package author and the package version attributes."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6407-missing-conformity-to-ihe-balp.yaml

@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 6407
+title: "Corrected IHE BALP AuditEvent generation, so that it records one Audit Event per resource owner. Thanks to Jens Villadsen (@jkiddo) for the contribution!"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/changes.yaml

@@ -0,0 +1,8 @@
+---
+- item:
+      type: "add"
+      title: "The version of a few dependencies have been bumped to more recent versions
+      (dependent HAPI modules listed in brackets):
+      <ul>
+      <li>org.hl7.fhir.core (Base): 6.3.25 -&gt; 6.4.0</li>
+      </ul>"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/version.yaml

@@ -0,0 +1,3 @@
+---
+release-date: "2025-02-17"
+codename: "TBD"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/clinical_reasoning/measures.md

@@ -111,8 +111,50 @@ A request using `periodStart` and `periodEnd` looks like:
 ```bash
 GET fhir/Measure/<MeasureId>/$evaluate-measure?periodStart=2019-01-01&periodEnd=2019-12-31
 ```
+`periodStart` and `periodEnd` support Dates (YYYY, YYYY-MM, or YYYY-MM-DD) and DateTimes (YYYY-MM-DDThh:mm:ss).  DateTime formats of YYYY-MM-DDThh:mm:ss+zz no longer accepted.  To pass in timezones to period queries, please see the [Headers](#headers) section below:
 
-`periodStart` and `periodEnd` support Dates (YYYY, YYYY-MM, or YYYY-MM-DD) and DateTimes (YYYY-MM-DDThh:mm:ss+zz:zz)
+#### Headers
+
+The behaviour of the  `periodStart` and `periodEnd` parameters depends on the value of the `Timezone` header.  The measure report will be queried according to the period range, as denoted by that timezone, **not the server timezone**.
+
+Accepted values for this header are documented on the [Wikipedia timezones page](https://en.wikipedia.org/wiki/List_of_tz_database_time_zones)
+
+ex:  `Timezone`:`America/Denver` will set the timezone to Mountain Time.
+
+If the client omits this header, the timezone will default to UTC.
+
+Please consult the below table for examples of various combinations of start, end, and timezone, as well as the resulting queried periods:
+
+| Request timezone   |          Start       |           End       | Converted Start           | Converted End             |
+|--------------------| ---------------------| --------------------|---------------------------|---------------------------|
+| (unset)            | (unset)              | (unset)             | N/A                       | N/A                       |
+| (unset)            | 2020                 | 2021                | 2020-01-01T00:00:00Z      | 2021-12-31T23:59:59Z      |
+| Z                  | 2020                 | 2021                | 2020-01-01T00:00:00Z      | 2021-12-31T23:59:59Z      |
+| UTC                | 2020                 | 2021                | 2020-01-01T00:00:00Z      | 2021-12-31T23:59:59Z      |
+| America/St_Johns   | 2020                 | 2021                | 2020-01-01T00:00:00-03:30 | 2021-12-31T23:59:59-03:30 |
+| America/Toronto    | 2020                 | 2021                | 2020-01-01T00:00:00-05:00 | 2021-12-31T23:59:59-05:00 |
+| America/Denver     | 2020                 | 2021                | 2020-01-01T00:00:00-07:00 | 2021-12-31T23:59:59-07:00 |
+| (unset)            | 2022-02              | 2022-08             | 2022-02-01T00:00:00Z      | 2022-08-31T23:59:59Z      |
+| UTC                | 2022-02              | 2022-08             | 2022-02-01T00:00:00Z      | 2022-08-31T23:59:59Z      |
+| America/St_Johns   | 2022-02              | 2022-08             | 2022-02-01T00:00:00-03:30 | 2022-08-31T23:59:59-02:30 |
+| America/Toronto    | 2022-02              | 2022-08             | 2022-02-01T00:00:00-05:00 | 2022-08-31T23:59:59-04:00 |
+| America/Denver     | 2022-02              | 2022-08             | 2022-02-01T00:00:00-07:00 | 2022-08-31T23:59:59-06:00 |
+| (unset)            | 2024-02-25           | 2024-02-26          | 2024-02-25T00:00:00Z      | 2024-02-26T23:59:59Z      |
+| UTC                | 2024-02-25           | 2024-02-26          | 2024-02-25T00:00:00Z      | 2024-02-26T23:59:59Z      |
+| America/St_Johns   | 2024-02-25           | 2024-02-26          | 2024-02-25T00:00:00-03:30 | 2024-02-26T23:59:59-03:30 |
+| America/Toronto    | 2024-02-25           | 2024-02-26          | 2024-02-25T00:00:00-05:00 | 2024-02-26T23:59:59-05:00 |
+| America/Denver     | 2024-02-25           | 2024-02-26          | 2024-02-25T00:00:00-07:00 | 2024-02-26T23:59:59-07:00 |
+| (unset)            | 2024-09-25           | 2024-09-26          | 2024-09-25T00:00:00Z      | 2024-09-26T23:59:59Z      |
+| UTC                | 2024-09-25           | 2024-09-26          | 2024-09-25T00:00:00Z      | 2024-09-26T23:59:59Z      |
+| America/St_Johns   | 2024-09-25           | 2024-09-26          | 2024-09-25T00:00:00-02:30 | 2024-09-26T23:59:59-02:30 |
+| America/Toronto    | 2024-09-25           | 2024-09-26          | 2024-09-25T00:00:00-04:00 | 2024-09-26T23:59:59-04:00 |
+| America/Denver     | 2024-09-25           | 2024-09-26          | 2024-09-25T00:00:00-06:00 | 2024-09-26T23:59:59-06:00 |
+| (unset)            | 2024-09-25T12:00:00  | 2024-09-26T12:00:00 | 2024-09-25T12:00:00-06:00 | 2024-09-26T11:59:59-06:00 |
+| Z                  | 2024-09-25T12:00:00  | 2024-09-26T12:00:00 | 2024-09-25T12:00:00-06:00 | 2024-09-26T11:59:59-06:00 |
+| UTC                | 2024-09-25T12:00:00  | 2024-09-26T12:00:00 | 2024-09-25T12:00:00-06:00 | 2024-09-26T11:59:59-06:00 |
+| America/St_Johns   | 2024-09-25T12:00:00  | 2024-09-26T12:00:00 | 2024-09-25T12:00:00-02:30 | 2024-09-26T11:59:59-02:30 |
+| America/Toronto    | 2024-09-25T12:00:00  | 2024-09-26T12:00:00 | 2024-09-25T12:00:00-04:00 | 2024-09-26T11:59:59-04:00 |
+| America/Denver     | 2024-09-25T12:00:00  | 2024-09-26T12:00:00 | 2024-09-25T12:00:00-06:00 | 2024-09-26T11:59:59-06:00 |
 
 #### Report Types
 

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/clinical_reasoning/plan_definitions.md

@@ -19,6 +19,7 @@ HAPI implements the following operations for PlanDefinitions:
 
 * [$apply](/docs/clinical_reasoning/plan_definitions.html#apply)
 * [$package](/docs/clinical_reasoning/plan_definitions.html#package)
+* [$data-requirements](/docs/clinical_reasoning/plan_definitions.html#datarequirements)
 
 ## Apply
 
@@ -40,32 +41,36 @@ GET http://your-server-base/fhir/PlanDefinition/opioidcds-10-patient-view/$apply
 
 The following parameters are supported for the `PlanDefinition/$apply` and `PlanDefinition/$r5.apply` operation:
 
-| Parameter           | Type                      | Description |
+| Parameter               | Type                      | Description |
-|---------------------|---------------------------|-------------|
+|-------------------------|---------------------------|-------------|
-| planDefinition      | PlanDefinition            | The plan definition to be applied. If the operation is invoked at the instance level, this parameter is not allowed; if the operation is invoked at the type level, this parameter is required, or a url (and optionally version) must be supplied. |
+| planDefinition          | PlanDefinition            | The plan definition to be applied. If the operation is invoked at the instance level, this parameter is not allowed; if the operation is invoked at the type level, this parameter is required, or a url (and optionally version) must be supplied. |
-| canonical           | canonical(PlanDefinition) | The canonical url of the plan definition to be applied. If the operation is invoked at the instance level, this parameter is not allowed; if the operation is invoked at the type level, this parameter (and optionally the version), or the planDefinition parameter must be supplied. |
+| canonical               | canonical(PlanDefinition) | The canonical url of the plan definition to be applied. If the operation is invoked at the instance level, this parameter is not allowed; if the operation is invoked at the type level, this parameter (and optionally the version), or the planDefinition parameter must be supplied. |
-| url                 | uri                       | Canonical URL of the PlanDefinition when invoked at the resource type level. This is exclusive with the planDefinition and canonical parameters. |
+| url                     | uri                       | Canonical URL of the PlanDefinition when invoked at the resource type level. This is exclusive with the planDefinition and canonical parameters. |
-| version             | string                    | Version of the PlanDefinition when invoked at the resource type level. This is exclusive with the planDefinition and canonical parameters. |
+| version                 | string                    | Version of the PlanDefinition when invoked at the resource type level. This is exclusive with the planDefinition and canonical parameters. |
-| subject             | string(reference)         | The subject(s) that is/are the target of the plan definition to be applied. |
+| subject                 | string(reference)         | The subject(s) that is/are the target of the plan definition to be applied. |
-| encounter           | string(reference)         | The encounter in context, if any. |
+| encounter               | string(reference)         | The encounter in context, if any. |
-| practitioner        | string(reference)         | The practitioner applying the plan definition. |
+| practitioner            | string(reference)         | The practitioner applying the plan definition. |
-| organization        | string(reference)         | The organization applying the plan definition. |
+| organization            | string(reference)         | The organization applying the plan definition. |
-| userType            | CodeableConcept           | The type of user initiating the request, e.g. patient, healthcare provider, or specific type of healthcare provider (physician, nurse, etc.) |
+| userType                | CodeableConcept           | The type of user initiating the request, e.g. patient, healthcare provider, or specific type of healthcare provider (physician, nurse, etc.) |
-| userLanguage        | CodeableConcept           | Preferred language of the person using the system |
+| userLanguage            | CodeableConcept           | Preferred language of the person using the system |
-| userTaskContext     | CodeableConcept           | The task the system user is performing, e.g. laboratory results review, medication list review, etc. This information can be used to tailor decision support outputs, such as recommended information resources. |
+| userTaskContext         | CodeableConcept           | The task the system user is performing, e.g. laboratory results review, medication list review, etc. This information can be used to tailor decision support outputs, such as recommended information resources. |
-| setting             | CodeableConcept           | The current setting of the request (inpatient, outpatient, etc.). |
+| setting                 | CodeableConcept           | The current setting of the request (inpatient, outpatient, etc.). |
-| settingContext      | CodeableConcept           | Additional detail about the setting of the request, if any |
+| settingContext          | CodeableConcept           | Additional detail about the setting of the request, if any |
-| parameters          | Parameters                | Any input parameters defined in libraries referenced by the PlanDefinition. |
+| parameters              | Parameters                | Any input parameters defined in libraries referenced by the PlanDefinition. |
-| useServerData       | boolean                   | Whether to use data from the server performing the evaluation. If this parameter is true (the default), then the operation will use data first from any bundles provided as parameters (through the data and prefetch parameters), second data from the server performing the operation, and third, data from the dataEndpoint parameter (if provided). If this parameter is false, the operation will use data first from the bundles provided in the data or prefetch parameters, and second from the dataEndpoint parameter (if provided). |
+| useServerData           | boolean                   | Whether to use data from the server performing the evaluation. If this parameter is true (the default), then the operation will use data first from any bundles provided as parameters (through the data and prefetch parameters), second data from the server performing the operation, and third, data from the dataEndpoint parameter (if provided). If this parameter is false, the operation will use data first from the bundles provided in the data or prefetch parameters, and second from the dataEndpoint parameter (if provided). |
-| data                | Bundle                    | Data to be made available to the PlanDefinition evaluation. |
+| data                    | Bundle                    | Data to be made available to the PlanDefinition evaluation. |
-| dataEndpoint        | Endpoint                  | An endpoint to use to access data referenced by retrieve operations in libraries referenced by the PlanDefinition. |
+| prefetchData            |                           | Data to be made available to the PlanDefinition evaluation, organized as prefetch response bundles. Each prefetchData parameter specifies either the name of the prefetchKey it is satisfying, a DataRequirement describing the prefetch, or both. |
-| contentEndpoint     | Endpoint                  | An endpoint to use to access content (i.e. libraries) referenced by the PlanDefinition. |
+| prefetchData.key        | string                    | The key of the prefetch item. This typically corresponds to the name of a parameter in a library, or the name of a prefetch item in a CDS Hooks discovery response. |
-| terminologyEndpoint | Endpoint                  | An endpoint to use to access terminology (i.e. valuesets, codesystems, and membership testing) referenced by the PlanDefinition. |
+| prefetchData.descriptor | DataRequirement           | A DataRequirement describing the content of the prefetch item. |
+| prefetchData.data       | Bundle                    | The prefetch data as a Bundle. If the prefetchData has no data part, it indicates there is no data associated with this prefetch item. |
+| dataEndpoint            | Endpoint                  | An endpoint to use to access data referenced by retrieve operations in libraries referenced by the PlanDefinition. |
+| contentEndpoint         | Endpoint                  | An endpoint to use to access content (i.e. libraries) referenced by the PlanDefinition. |
+| terminologyEndpoint     | Endpoint                  | An endpoint to use to access terminology (i.e. valuesets, codesystems, and membership testing) referenced by the PlanDefinition. |
 
 
 ## Package
 
-The `PlanDefinition/$package` [operation](https://build.fhir.org/ig/HL7/crmi-ig/OperationDefinition-crmi-package.html) for PlanDefinition will generate a Bundle of resources that includes the PlanDefinition as well as any related resources which can then be shared. This implementation follows the [CRMI IG](https://build.fhir.org/ig/HL7/crmi-ig/branches/master/index.html) guidance for [packaging artifacts](https://build.fhir.org/ig/HL7/crmi-ig/branches/master/packaging.html).
+The `PlanDefinition/$package` [operation](https://hl7.org/fhir/uv/crmi/OperationDefinition-crmi-package.html) for PlanDefinition will generate a Bundle of resources that includes the PlanDefinition as well as any related resources which can then be shared. This implementation follows the [CRMI IG](https://hl7.org/fhir/uv/crmi/index.html) guidance for [packaging artifacts](https://hl7.org/fhir/uv/crmi/packaging.html).
 
 ### Parameters
 
@@ -80,6 +85,22 @@ The following parameters are supported for the `PlanDefinition/$package` operati
 | usePut    | boolean   | Determines the type of method returned in the Bundle Entries: POST if False (the default), PUT if True. | 
 
 
+## DataRequirements
+
+The `PlanDefinition/$data-requirements` [operation](https://hl7.org/fhir/uv/crmi/OperationDefinition-crmi-data-requirements.html) for PlanDefinition will generate a Library of type `module-definition` that returns the computed effective requirements of the artifact.
+
+### Parameters
+
+The following parameters are supported for the `PlanDefinition/$data-requirements` operation:
+
+| Parameter | Type      | Description                                                                                                    |
+|-----------|-----------|----------------------------------------------------------------------------------------------------------------|
+| id        | string    | The logical id of the canonical or artifact resource to analyze.                                               |
+| canonical | canonical | A canonical url (optionally version specific) to a canonical resource.                                         |
+| url       | uri       | A canonical or artifact reference to a canonical resource. This is exclusive with the canonical parameter.     |
+| version   | string    | The version of the canonical or artifact resource to analyze. This is exclusive with the canonical parameter.  |
+
+
 ## Example PlanDefinition
 
 ```json

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/clinical_reasoning/questionnaires.md

@@ -16,7 +16,7 @@ HAPI implements the following operations for Questionnaires and QuestionnaireRes
 * [$populate](/docs/clinical_reasoning/questionnaires.html#populate)
 * [$extract](/docs/clinical_reasoning/questionnaires.html#extract)
 * [$package](/docs/clinical_reasoning/questionnaires.html#package)
-
+* [$data-requirements](/docs/clinical_reasoning/questionnaires.html#datarequirements)
 
 ## Questionnaire
 
@@ -26,65 +26,69 @@ The `StructureDefinition/$questionnaire` [operation]() generates a [Questionnair
 
 The following parameters are supported for the `StructureDefinition/$questionnaire` operation:
 
-| Parameter | Type | Description |
+| Parameter           | Type                 | Description |
-|-----------|------|-------------|
+|---------------------|----------------------|-------------|
-| profile          | StructureDefinition      | The StructureDefinition to base the Questionnaire on. Used when the operation is invoked at the 'type' level. |
+| profile             | StructureDefinition  | The StructureDefinition to base the Questionnaire on. Used when the operation is invoked at the 'type' level.                                  |
-| canonical | canonical | The canonical identifier for the StructureDefinition (optionally version-specific). |
+| canonical           | canonical            | The canonical identifier for the StructureDefinition (optionally version-specific).                                                            |
-| url | uri | Canonical URL of the StructureDefinition when invoked at the resource type level. This is exclusive with the profile and canonical parameters. |
+| url                 | uri                  | Canonical URL of the StructureDefinition when invoked at the resource type level. This is exclusive with the profile and canonical parameters. |
-| version | string | Version of the StructureDefinition when invoked at the resource type level. This is exclusive with the profile and canonical parameters. |
+| version             | string               | Version of the StructureDefinition when invoked at the resource type level. This is exclusive with the profile and canonical parameters.       |
-| supportedOnly | boolean | If true (default: false), the questionnaire will only include those elements marked as "mustSupport='true'" in the StructureDefinition. |
+| supportedOnly       | boolean              | If true (default: false), the questionnaire will only include those elements marked as "mustSupport='true'" in the StructureDefinition.        |
-| requiredOnly | boolean | If true (default: false), the questionnaire will only include those elements marked as "min>0" in the StructureDefinition. |
+| requiredOnly        | boolean              | If true (default: false), the questionnaire will only include those elements marked as "min>0" in the StructureDefinition.                     |
-| subject | string | The subject(s) that is/are the target of the Questionnaire. |
+| contentEndpoint     | Endpoint             | An endpoint to use to access content (i.e. libraries) referenced by the StructureDefinition.                                                   |
-| parameters | Parameters | Any input parameters defined in libraries referenced by the StructureDefinition. |
+| terminologyEndpoint | Endpoint             | An endpoint to use to access terminology (i.e. valuesets, codesystems, and membership testing) referenced by the StructureDefinition.          |
-| useServerData | boolean Whether to use data from the server performing the evaluation. |
-| data | Bundle | Data to be made available during CQL evaluation. |
-| dataEndpoint | Endpoint | An endpoint to use to access data referenced by retrieve operations in libraries referenced by the StructureDefinition. |
-| contentEndpoint | Endpoint | An endpoint to use to access content (i.e. libraries) referenced by the StructureDefinition. |
-| terminologyEndpoint | Endpoint | An endpoint to use to access terminology (i.e. valuesets, codesystems, and membership testing) referenced by the StructureDefinition. |
 
 ## Populate
 
-The `Questionnaire/$populate` [operation](https://hl7.org/fhir/uv/sdc/OperationDefinition-Questionnaire-populate.html) generates a [QuestionnaireResponse](https://www.hl7.org/fhir/questionnaireresponse.html) based on a specific [Questionnaire](https://www.hl7.org/fhir/questionnaire.html), filling in answers to questions where possible based on information provided as part of the operation or already known by the server about the subject of the Questionnaire. 
+The `Questionnaire/$populate` [operation](https://hl7.org/fhir/uv/sdc/OperationDefinition-Questionnaire-populate.html) generates a [QuestionnaireResponse](https://www.hl7.org/fhir/questionnaireresponse.html) based on a specific [Questionnaire](https://www.hl7.org/fhir/questionnaire.html), filling in answers to questions where possible based on information provided as part of the operation or already known by the server about the subject of the Questionnaire.  
+
+This implementation only allows for [Expression-based](https://hl7.org/fhir/uv/sdc/populate.html#expression-based-population) population.
+Additional parameters have been added to support CQL evaluation.
 
 ### Parameters
 
 The following parameters are supported for the `Questionnaire/$populate` operation:
 
-| Parameter | Type | Description |
+| Parameter           | Type          | Description |
-|-----------|------|-------------|
+|---------------------|---------------|-------------|
-| questionnaire | Questionnaire | The Questionnaire to populate. Used when the operation is invoked at the 'type' level. |
+| questionnaire       | Questionnaire | The Questionnaire to populate. Used when the operation is invoked at the 'type' level. |
-| canonical | canonical | The canonical identifier for the Questionnaire (optionally version-specific). |
+| canonical           | canonical     | The canonical identifier for the Questionnaire (optionally version-specific). |
-| url | uri | Canonical URL of the Questionnaire when invoked at the resource type level. This is exclusive with the questionnaire and canonical parameters. |
+| url                 | uri           | Canonical URL of the Questionnaire when invoked at the resource type level. This is exclusive with the questionnaire and canonical parameters. |
-| version | string | Version of the Questionnaire when invoked at the resource type level. This is exclusive with the questionnaire and canonical parameters. |
+| version             | string        | Version of the Questionnaire when invoked at the resource type level. This is exclusive with the questionnaire and canonical parameters. |
-| subject | string | The subject(s) that is/are the target of the Questionnaire. |
+| subject             | Reference     | The resource that is to be the QuestionnaireResponse.subject. The QuestionnaireResponse instance will reference the provided subject. |
-| parameters | Parameters | Any input parameters defined in libraries referenced by the Questionnaire. |
+| context             |               | Resources containing information to be used to help populate the QuestionnaireResponse. | 
-| useServerData | boolean | Whether to use data from the server performing the evaluation. |
+| context.name        | string        | The name of the launchContext or root Questionnaire variable the passed content should be used as for population purposes. The name SHALL correspond to a launchContext or variable delared at the root of the Questionnaire. | 
-| data | Bundle | Data to be made available during CQL evaluation. |
+| context.reference   | Reference     | The actual resource (or resources) to use as the value of the launchContext or variable. | 
-| dataEndpoint | Endpoint | An endpoint to use to access data referenced by retrieve operations in libraries referenced by the Questionnaire. |
+| local               | boolean       | Whether the server should use what resources and other knowledge it has about the referenced subject when pre-populating answers to questions. |
-| contentEndpoint | Endpoint | An endpoint to use to access content (i.e. libraries) referenced by the Questionnaire. |
+| launchContext       | Extension     | The [Questionnaire Launch Context](https://hl7.org/fhir/uv/sdc/StructureDefinition-sdc-questionnaire-launchContext.html) extension containing Resources that provide context for form processing logic (pre-population) when creating/displaying/editing a QuestionnaireResponse. |
-| terminologyEndpoint | Endpoint | An endpoint to use to access terminology (i.e. valuesets, codesystems, and membership testing) referenced by the Questionnaire. |
+| parameters          | Parameters    | Any input parameters defined in libraries referenced by the Questionnaire. |
-
+| useServerData       | boolean       | Whether to use data from the server performing the evaluation. |
-
+| data                | Bundle        | Data to be made available during CQL evaluation. |
+| dataEndpoint        | Endpoint      | An endpoint to use to access data referenced by retrieve operations in libraries referenced by the Questionnaire. |
+| contentEndpoint     | Endpoint      | An endpoint to use to access content (i.e. libraries) referenced by the Questionnaire. |
+| terminologyEndpoint | Endpoint      | An endpoint to use to access terminology (i.e. valuesets, codesystems, and membership testing) referenced by the Questionnaire. |
+ 
 ## Extract
 
 The `QuestionnaireResponse/$extract` [operation](http://hl7.org/fhir/uv/sdc/OperationDefinition-QuestionnaireResponse-extract.html) takes a completed [QuestionnaireResponse](https://www.hl7.org/fhir/questionnaireresponse.html) and converts it to a Bundle of resources by using metadata embedded in the [Questionnaire](https://www.hl7.org/fhir/questionnaire.html) the QuestionnaireResponse is based on. The extracted resources might include Observations, MedicationStatements and other standard FHIR resources which can then be shared and manipulated. When invoking the $extract operation, care should be taken that the submitted QuestionnaireResponse is itself valid. If not, the extract operation could fail (with appropriate OperationOutcomes) or, more problematic, might succeed but provide incorrect output.
 
-This implementation allows for both [Observation based](https://hl7.org/fhir/uv/sdc/extraction.html#observation-based-extraction) and [Definition based](https://hl7.org/fhir/uv/sdc/extraction.html#definition-based-extraction) extraction.
+This implementation allows for both [Observation-based](https://hl7.org/fhir/uv/sdc/extraction.html#observation-based-extraction) and [Definition-based](https://hl7.org/fhir/uv/sdc/extraction.html#definition-based-extraction) extraction.
 
 ### Parameters
 
 The following parameters are supported for the `QuestionnaireResponse/$extract` operation:
 
-| Parameter | Type | Description |
+| Parameter              | Type                  | Description |
-|-----------|------|-------------|
+|------------------------|-----------------------|-------------|
 | questionnaire-response | QuestionnaireResponse | The QuestionnaireResponse to extract data from. Used when the operation is invoked at the 'type' level. |
-| parameters | Parameters | Any input parameters defined in libraries referenced by the Questionnaire. |
+| questionnaire          | Questionnaire         | The Questionnaire the QuestionnaireResponse is answering.  Used when the server does not have access to the Questionnaire. |
-| data | Bundle | Data to be made available during CQL evaluation. |
+| parameters             | Parameters            | Any input parameters defined in libraries referenced by the Questionnaire. |
+| useServerData          | boolean               | Whether to use data from the server performing the evaluation. |
+| data                   | Bundle                | Data to be made available during CQL evaluation. |
 
 
 ## Package
 
-The `Questionnaire/$package` [operation](https://build.fhir.org/ig/HL7/crmi-ig/OperationDefinition-crmi-package.html) for [Questionnaire](https://www.hl7.org/fhir/questionnaire.html) will generate a Bundle of resources that includes the Questionnaire as well as any related Library or ValueSet resources which can then be shared. This implementation follows the [CRMI IG](https://build.fhir.org/ig/HL7/crmi-ig/branches/master/index.html) guidance for [packaging artifacts](https://build.fhir.org/ig/HL7/crmi-ig/branches/master/packaging.html).
+The `Questionnaire/$package` [operation](https://hl7.org/fhir/uv/crmi/OperationDefinition-crmi-package.html) for [Questionnaire](https://www.hl7.org/fhir/questionnaire.html) will generate a Bundle of resources that includes the Questionnaire as well as any related Library or ValueSet resources which can then be shared. This implementation follows the [CRMI IG](https://hl7.org/fhir/uv/crmi/index.html) guidance for [packaging artifacts](https://hl7.org/fhir/uv/crmi/packaging.html).
 
 ### Parameters
 
@@ -99,6 +103,22 @@ The following parameters are supported for the `Questionnaire/$package` operatio
 | usePut    | boolean   | Determines the type of method returned in the Bundle Entries: POST if False (the default), PUT if True. | 
 
 
+## DataRequirements
+
+The `Questionnaire/$data-requirements` [operation](https://hl7.org/fhir/uv/crmi/OperationDefinition-crmi-data-requirements.html) for Questionnaire will generate a Library of type `module-definition` that returns the computed effective requirements of the artifact.
+
+### Parameters
+
+The following parameters are supported for the `Questionnaire/$data-requirements` operation:
+
+| Parameter | Type      | Description                                                                                                    |
+|-----------|-----------|----------------------------------------------------------------------------------------------------------------|
+| id        | string    | The logical id of the canonical or artifact resource to analyze.                                               |
+| canonical | canonical | A canonical url (optionally version specific) to a canonical resource.                                         |
+| url       | uri       | A canonical or artifact reference to a canonical resource. This is exclusive with the canonical parameter.     |
+| version   | string    | The version of the canonical or artifact resource to analyze. This is exclusive with the canonical parameter.  |
+
+
 ## Example Questionnaire
 
 ```json

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/contributing/hacking_guide.md

@@ -51,6 +51,14 @@ HAPI is built primary using	[Apache Maven](http://maven.apache.org/). Even if yo
 [INFO] Finished at: 2016-02-27T15:05:35+00:00
 ```
 
+# Rebuilding the Database Schema
+
+Database schema is built as part of your maven build, but in case you need to rebuild it later, you can use the command:
+
+   ```bash
+   mvn hapi-tinder:generate-ddl
+   ```
+
 # Troubleshooting
 
 If the build fails to execute successfully, try the following:

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/files.properties

@@ -94,6 +94,7 @@ page.clinical_reasoning.overview=Clinical Reasoning Overview
 page.clinical_reasoning.cql=CQL
 page.clinical_reasoning.caregaps=Care Gaps
 page.clinical_reasoning.measures=Measures
+page.clinical_reasoning.activity_definitions=ActivityDefinitions
 page.clinical_reasoning.plan_definitions=PlanDefinitions
 page.clinical_reasoning.questionnaires=Questionnaires
 

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/search.md

@@ -238,3 +238,7 @@ In order to improve sorting performance when chained sorts are needed, an [Uplif
 # _include and _revinclude order
 
 By default, all _revincludes will be performed first and then all _includes are performed afterwards.  However, if any _revinclude parameters are modified with :iterate (or :recurse for earlier versions of FHIR) then all _include parameters will be evaluated first.
+
+# Custom Search Parameters
+
+HAPI FHIR has the ability to index and use custom search parameters, including parameters which enforce uniqueness, parametrs which index combinations of parameters, and parameters which are indexed but not used for searches until they are ready. See [Custom Search Parameters](https://smilecdr.com/docs/fhir_standard/fhir_search_custom_search_parameters.html) for more information.

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_batch/introduction.md

@@ -70,3 +70,7 @@ If a Job Definition is set to having Gated Execution, then all work chunks for a
 ### Job Instance Completion
 
 A Batch Job Maintenance Service runs every minute to monitor the status of all Job Instances and the Job Instance is transitioned to either `COMPLETED`, `ERRORED` or `FAILED` according to the status of all outstanding work chunks for that job instance. If the job instance is still `IN_PROGRESS` this maintenance service also estimates the time remaining to complete the job.
+
+## Logging
+
+The job instance ID and work chunk ID are both available through the logback MDC and can be accessed using the `%X` specifier in a `logback.xml` file. See [Logging](/docs/appendix/logging.html#logging) for more details about logging in HAPI. 

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_plain/rest_operations_search.md

@@ -287,7 +287,7 @@ Dates are a special case, since it is a fairly common scenario to want to match
 
 # Resource Includes (_include)
 
-FHIR allows clients to request that specific linked resources be included as contained resources, which means that they will be "embedded" in a special container called "contained" within the parent resource.
+Using the `_include` FHIR parameter, clients can request that specific linked resources be embedded directly within search results. These included resources will have a search.mode of "include".
 
 HAPI allows you to add a parameter for accepting includes if you wish to support them for specific search methods.
 

hapi-fhir-jacoco/pom.xml

@@ -11,7 +11,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.1-SNAPSHOT</version>
+		<version>7.7.3-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jaxrsserver-base/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.1-SNAPSHOT</version>
+		<version>7.7.3-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/client/GenericJaxRsClientDstu2Test.java

@@ -1474,7 +1474,9 @@ public class GenericJaxRsClientDstu2Test {
 			.execute();
 
 
-		assertEquals(ourServer.getBaseUrl() + "/fhir/Patient/_search?_elements=identifier%2Cname", CAPTURE_SERVLET.ourRequestUri);
+		assertThat(CAPTURE_SERVLET.ourRequestUri).isIn(
+			ourServer.getBaseUrl() + "/fhir/Patient/_search?_elements=identifier%2Cname",
+			ourServer.getBaseUrl() + "/fhir/Patient/_search?_elements=name%2Cidentifier");
 
 		//		assertThat(MY_SERVLET.ourRequestUri,
 		//				either(equalTo(ourServer.getBaseUrl() + "/fhir/Patient?name=james&_elements=name%2Cidentifier")).or(equalTo(ourServer.getBaseUrl() + "/fhir/Patient?name=james&_elements=identifier%2Cname")));
@@ -1511,7 +1513,10 @@ public class GenericJaxRsClientDstu2Test {
 
 
 		assertThat(CAPTURE_SERVLET.ourRequestUri).contains(ourServer.getBaseUrl() + "/fhir/Patient/_search?");
-		assertThat(CAPTURE_SERVLET.ourRequestUri).contains("_elements=identifier%2Cname");
+		assertThat(CAPTURE_SERVLET.ourRequestUri).satisfiesAnyOf(
+			s -> assertThat(s).contains("_elements=identifier%2Cname"),
+			s -> assertThat(s).contains("_elements=name%2Cidentifier")
+		);
 
 		//		assertThat(MY_SERVLET.ourRequestUri,
 		//				either(equalTo(ourServer.getBaseUrl() + "/fhir/Patient?name=james&_elements=name%2Cidentifier")).or(equalTo(ourServer.getBaseUrl() + "/fhir/Patient?name=james&_elements=identifier%2Cname")));

hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/client/GenericJaxRsClientDstu3Test.java

@@ -1546,7 +1546,9 @@ public class GenericJaxRsClientDstu3Test {
 			.execute();
 		//@formatter:on
 
-		assertEquals(ourServer.getBaseUrl() + "/fhir/Patient/_search?_elements=identifier%2Cname", MY_SERVLET.ourRequestUri);
+		assertThat(MY_SERVLET.ourRequestUri).isIn(
+			ourServer.getBaseUrl() + "/fhir/Patient/_search?_elements=identifier%2Cname",
+			ourServer.getBaseUrl() + "/fhir/Patient/_search?_elements=name%2Cidentifier");
 
 		//		assertThat(MY_SERVLET.ourRequestUri,
 		//				either(equalTo(ourServer.getBaseUrl() + "/fhir/Patient?name=james&_elements=name%2Cidentifier")).or(equalTo(ourServer.getBaseUrl() + "/fhir/Patient?name=james&_elements=identifier%2Cname")));
@@ -1583,7 +1585,10 @@ public class GenericJaxRsClientDstu3Test {
 		//@formatter:on
 
 		assertThat(MY_SERVLET.ourRequestUri).contains(ourServer.getBaseUrl() + "/fhir/Patient/_search?");
-		assertThat(MY_SERVLET.ourRequestUri).contains("_elements=identifier%2Cname");
+		assertThat(MY_SERVLET.ourRequestUri).satisfiesAnyOf(
+			s -> assertThat(s).contains("_elements=identifier%2Cname"),
+			s -> assertThat(s).contains("_elements=name%2Cidentifier")
+		);
 
 		//		assertThat(MY_SERVLET.ourRequestUri,
 		//				either(equalTo(ourServer.getBaseUrl() + "/fhir/Patient?name=james&_elements=name%2Cidentifier")).or(equalTo(ourServer.getBaseUrl() + "/fhir/Patient?name=james&_elements=identifier%2Cname")));

hapi-fhir-jpa/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.1-SNAPSHOT</version>
+		<version>7.7.3-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.1-SNAPSHOT</version>
+		<version>7.7.3-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
@@ -414,7 +414,6 @@
 			<plugin>
 				<groupId>ca.uhn.hapi.fhir</groupId>
 				<artifactId>hapi-tinder-plugin</artifactId>
-				<version>${project.version}</version>
 				<executions>
 					<execution>
 						<id>build_dstu2</id>
@@ -525,7 +524,6 @@
 			<plugin>
 				<groupId>ca.uhn.hapi.fhir</groupId>
 				<artifactId>hapi-tinder-plugin</artifactId>
-				<version>${project.version}</version>
 				<executions>
 					<execution>
 						<goals>
@@ -534,6 +532,7 @@
 					</execution>
 				</executions>
 				<configuration>
+					<skip>false</skip>
 					<packageNames>
 						<packageName>ca.uhn.fhir.jpa.entity</packageName>
 						<packageName>ca.uhn.fhir.jpa.model.entity</packageName>

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch2/JpaJobPersistenceImpl.java

@@ -21,6 +21,8 @@ package ca.uhn.fhir.jpa.batch2;
 
 import ca.uhn.fhir.batch2.api.IJobPersistence;
 import ca.uhn.fhir.batch2.api.JobOperationResultJson;
+import ca.uhn.fhir.batch2.model.BatchInstanceStatusDTO;
+import ca.uhn.fhir.batch2.model.BatchWorkChunkStatusDTO;
 import ca.uhn.fhir.batch2.model.FetchJobInstancesRequest;
 import ca.uhn.fhir.batch2.model.JobInstance;
 import ca.uhn.fhir.batch2.model.StatusEnum;
@@ -258,6 +260,22 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
 				.execute(() -> myJobInstanceRepository.findById(theInstanceId).map(this::toInstance));
 	}
 
+	@Nonnull
+	@Override
+	public List<BatchWorkChunkStatusDTO> fetchWorkChunkStatusForInstance(String theInstanceId) {
+		return myTransactionService
+				.withSystemRequestOnDefaultPartition()
+				.execute(() -> myWorkChunkRepository.fetchWorkChunkStatusForInstance(theInstanceId));
+	}
+
+	@Nonnull
+	@Override
+	public BatchInstanceStatusDTO fetchBatchInstanceStatus(String theInstanceId) {
+		return myTransactionService
+				.withSystemRequestOnDefaultPartition()
+				.execute(() -> myJobInstanceRepository.fetchBatchInstanceStatus(theInstanceId));
+	}
+
 	@Override
 	@Transactional(propagation = Propagation.REQUIRES_NEW)
 	public List<JobInstance> fetchInstances(FetchJobInstancesRequest theRequest, int thePage, int theBatchSize) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/JpaBulkExportProcessor.java

@@ -625,7 +625,8 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor<JpaPid> {
 			resourceToCheck = "Patient";
 			activeSearchParamName = "organization";
 		}
-		return mySearchParamRegistry.getActiveSearchParam(resourceToCheck, activeSearchParamName);
+		return mySearchParamRegistry.getActiveSearchParam(
+				resourceToCheck, activeSearchParamName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
 	}
 
 	/**

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

@@ -43,6 +43,7 @@ import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
 import ca.uhn.fhir.jpa.bulk.imprt.svc.BulkDataImportSvcImpl;
 import ca.uhn.fhir.jpa.cache.IResourceVersionSvc;
 import ca.uhn.fhir.jpa.cache.ResourceVersionSvcDaoImpl;
+import ca.uhn.fhir.jpa.dao.CacheTagDefinitionDao;
 import ca.uhn.fhir.jpa.dao.DaoSearchParamProvider;
 import ca.uhn.fhir.jpa.dao.HistoryBuilder;
 import ca.uhn.fhir.jpa.dao.HistoryBuilderFactory;
@@ -56,6 +57,7 @@ import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
 import ca.uhn.fhir.jpa.dao.TransactionProcessor;
 import ca.uhn.fhir.jpa.dao.data.IResourceModifiedDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceSearchUrlDao;
+import ca.uhn.fhir.jpa.dao.data.ITagDefinitionDao;
 import ca.uhn.fhir.jpa.dao.expunge.ExpungeEverythingService;
 import ca.uhn.fhir.jpa.dao.expunge.ExpungeOperation;
 import ca.uhn.fhir.jpa.dao.expunge.ExpungeService;
@@ -377,17 +379,17 @@ public class JpaConfig {
 
 	@Bean
 	public TaskScheduler taskScheduler() {
-		ConcurrentTaskScheduler retVal = new ConcurrentTaskScheduler();
+		ConcurrentTaskScheduler retVal = new ConcurrentTaskScheduler(
-		retVal.setConcurrentExecutor(scheduledExecutorService().getObject());
+				scheduledExecutorService().getObject(),
-		retVal.setScheduledExecutor(scheduledExecutorService().getObject());
+				scheduledExecutorService().getObject());
 		return retVal;
 	}
 
 	@Bean(name = TASK_EXECUTOR_NAME)
 	public AsyncTaskExecutor taskExecutor() {
-		ConcurrentTaskScheduler retVal = new ConcurrentTaskScheduler();
+		ConcurrentTaskScheduler retVal = new ConcurrentTaskScheduler(
-		retVal.setConcurrentExecutor(scheduledExecutorService().getObject());
+				scheduledExecutorService().getObject(),
-		retVal.setScheduledExecutor(scheduledExecutorService().getObject());
+				scheduledExecutorService().getObject());
 		return retVal;
 	}
 
@@ -893,4 +895,10 @@ public class JpaConfig {
 			FhirContext theFhirContext, HibernatePropertiesProvider theHibernatePropertiesProvider) {
 		return new ResourceHistoryCalculator(theFhirContext, theHibernatePropertiesProvider.isOracleDialect());
 	}
+
+	@Bean
+	public CacheTagDefinitionDao tagDefinitionDao(
+			ITagDefinitionDao tagDefinitionDao, MemoryCacheService memoryCacheService) {
+		return new CacheTagDefinitionDao(tagDefinitionDao, memoryCacheService);
+	}
 }

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

@@ -75,7 +75,6 @@ import ca.uhn.fhir.jpa.searchparam.matcher.InMemoryResourceMatcher;
 import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
 import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
 import ca.uhn.fhir.jpa.util.AddRemoveCount;
-import ca.uhn.fhir.jpa.util.MemoryCacheService;
 import ca.uhn.fhir.jpa.util.QueryChunker;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
@@ -89,7 +88,6 @@ import ca.uhn.fhir.rest.api.InterceptorInvocationTimingEnum;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
-import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
@@ -107,14 +105,8 @@ import jakarta.annotation.Nonnull;
 import jakarta.annotation.Nullable;
 import jakarta.annotation.PostConstruct;
 import jakarta.persistence.EntityManager;
-import jakarta.persistence.NoResultException;
 import jakarta.persistence.PersistenceContext;
 import jakarta.persistence.PersistenceContextType;
-import jakarta.persistence.TypedQuery;
-import jakarta.persistence.criteria.CriteriaBuilder;
-import jakarta.persistence.criteria.CriteriaQuery;
-import jakarta.persistence.criteria.Predicate;
-import jakarta.persistence.criteria.Root;
 import org.apache.commons.lang3.NotImplementedException;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
@@ -136,19 +128,11 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationContext;
 import org.springframework.context.ApplicationContextAware;
 import org.springframework.stereotype.Repository;
-import org.springframework.transaction.PlatformTransactionManager;
-import org.springframework.transaction.TransactionDefinition;
-import org.springframework.transaction.TransactionStatus;
-import org.springframework.transaction.support.TransactionCallback;
-import org.springframework.transaction.support.TransactionSynchronization;
-import org.springframework.transaction.support.TransactionSynchronizationManager;
-import org.springframework.transaction.support.TransactionTemplate;
 
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.Date;
-import java.util.HashMap;
 import java.util.HashSet;
 import java.util.IdentityHashMap;
 import java.util.List;
@@ -158,7 +142,6 @@ import java.util.stream.Collectors;
 import javax.xml.stream.events.Characters;
 import javax.xml.stream.events.XMLEvent;
 
-import static java.util.Objects.isNull;
 import static java.util.Objects.nonNull;
 import static org.apache.commons.collections4.CollectionUtils.isEqualCollection;
 import static org.apache.commons.lang3.StringUtils.isBlank;
@@ -182,8 +165,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 	public static final long INDEX_STATUS_INDEXED = 1L;
 	public static final long INDEX_STATUS_INDEXING_FAILED = 2L;
 	public static final String NS_JPA_PROFILE = "https://github.com/hapifhir/hapi-fhir/ns/jpa/profile";
-	// total attempts to do a tag transaction
-	private static final int TOTAL_TAG_READ_ATTEMPTS = 10;
 	private static final Logger ourLog = LoggerFactory.getLogger(BaseHapiFhirDao.class);
 	private static boolean ourValidationDisabledForUnitTest;
 	private static boolean ourDisableIncrementOnUpdateForUnitTest = false;
@@ -248,17 +229,14 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 	@Autowired
 	private IPartitionLookupSvc myPartitionLookupSvc;
 
-	@Autowired
-	private MemoryCacheService myMemoryCacheService;
-
 	@Autowired(required = false)
 	private IFulltextSearchSvc myFulltextSearchSvc;
 
 	@Autowired
-	private PlatformTransactionManager myTransactionManager;
+	protected ResourceHistoryCalculator myResourceHistoryCalculator;
 
 	@Autowired
-	protected ResourceHistoryCalculator myResourceHistoryCalculator;
+	protected CacheTagDefinitionDao cacheTagDefinitionDao;
 
 	protected final CodingSpy myCodingSpy = new CodingSpy();
 
@@ -307,7 +285,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		TagList tagList = ResourceMetadataKeyEnum.TAG_LIST.get(theResource);
 		if (tagList != null) {
 			for (Tag next : tagList) {
-				TagDefinition def = getTagOrNull(
+				TagDefinition def = cacheTagDefinitionDao.getTagOrNull(
 						theTransactionDetails,
 						TagTypeEnum.TAG,
 						next.getScheme(),
@@ -326,7 +304,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		List<BaseCodingDt> securityLabels = ResourceMetadataKeyEnum.SECURITY_LABELS.get(theResource);
 		if (securityLabels != null) {
 			for (BaseCodingDt next : securityLabels) {
-				TagDefinition def = getTagOrNull(
+				TagDefinition def = cacheTagDefinitionDao.getTagOrNull(
 						theTransactionDetails,
 						TagTypeEnum.SECURITY_LABEL,
 						next.getSystemElement().getValue(),
@@ -345,7 +323,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		List<IdDt> profiles = ResourceMetadataKeyEnum.PROFILES.get(theResource);
 		if (profiles != null) {
 			for (IIdType next : profiles) {
-				TagDefinition def = getTagOrNull(
+				TagDefinition def = cacheTagDefinitionDao.getTagOrNull(
 						theTransactionDetails, TagTypeEnum.PROFILE, NS_JPA_PROFILE, next.getValue(), null, null, null);
 				if (def != null) {
 					ResourceTag tag = theEntity.addTag(def);
@@ -364,7 +342,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		List<? extends IBaseCoding> tagList = theResource.getMeta().getTag();
 		if (tagList != null) {
 			for (IBaseCoding next : tagList) {
-				TagDefinition def = getTagOrNull(
+				TagDefinition def = cacheTagDefinitionDao.getTagOrNull(
 						theTransactionDetails,
 						TagTypeEnum.TAG,
 						next.getSystem(),
@@ -383,7 +361,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		List<? extends IBaseCoding> securityLabels = theResource.getMeta().getSecurity();
 		if (securityLabels != null) {
 			for (IBaseCoding next : securityLabels) {
-				TagDefinition def = getTagOrNull(
+				TagDefinition def = cacheTagDefinitionDao.getTagOrNull(
 						theTransactionDetails,
 						TagTypeEnum.SECURITY_LABEL,
 						next.getSystem(),
@@ -402,7 +380,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		List<? extends IPrimitiveType<String>> profiles = theResource.getMeta().getProfile();
 		if (profiles != null) {
 			for (IPrimitiveType<String> next : profiles) {
-				TagDefinition def = getTagOrNull(
+				TagDefinition def = cacheTagDefinitionDao.getTagOrNull(
 						theTransactionDetails, TagTypeEnum.PROFILE, NS_JPA_PROFILE, next.getValue(), null, null, null);
 				if (def != null) {
 					ResourceTag tag = theEntity.addTag(def);
@@ -422,7 +400,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		if (!def.isStandardType()) {
 			String profile = def.getResourceProfile("");
 			if (isNotBlank(profile)) {
-				TagDefinition profileDef = getTagOrNull(
+				TagDefinition profileDef = cacheTagDefinitionDao.getTagOrNull(
 						theTransactionDetails, TagTypeEnum.PROFILE, NS_JPA_PROFILE, profile, null, null, null);
 
 				ResourceTag tag = theEntity.addTag(profileDef);
@@ -456,164 +434,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		myContext = theContext;
 	}
 
-	/**
-	 * <code>null</code> will only be returned if the scheme and tag are both blank
-	 */
-	protected TagDefinition getTagOrNull(
-			TransactionDetails theTransactionDetails,
-			TagTypeEnum theTagType,
-			String theScheme,
-			String theTerm,
-			String theLabel,
-			String theVersion,
-			Boolean theUserSelected) {
-		if (isBlank(theScheme) && isBlank(theTerm) && isBlank(theLabel)) {
-			return null;
-		}
-
-		MemoryCacheService.TagDefinitionCacheKey key =
-				toTagDefinitionMemoryCacheKey(theTagType, theScheme, theTerm, theVersion, theUserSelected);
-
-		TagDefinition retVal = myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.TAG_DEFINITION, key);
-		if (retVal == null) {
-			HashMap<MemoryCacheService.TagDefinitionCacheKey, TagDefinition> resolvedTagDefinitions =
-					theTransactionDetails.getOrCreateUserData(
-							HapiTransactionService.XACT_USERDATA_KEY_RESOLVED_TAG_DEFINITIONS, HashMap::new);
-
-			retVal = resolvedTagDefinitions.get(key);
-
-			if (retVal == null) {
-				// actual DB hit(s) happen here
-				retVal = getOrCreateTag(theTagType, theScheme, theTerm, theLabel, theVersion, theUserSelected);
-
-				TransactionSynchronization sync = new AddTagDefinitionToCacheAfterCommitSynchronization(key, retVal);
-				TransactionSynchronizationManager.registerSynchronization(sync);
-
-				resolvedTagDefinitions.put(key, retVal);
-			}
-		}
-
-		return retVal;
-	}
-
-	/**
-	 * Gets the tag defined by the fed in values, or saves it if it does not
-	 * exist.
-	 * <p>
-	 * Can also throw an InternalErrorException if something bad happens.
-	 */
-	private TagDefinition getOrCreateTag(
-			TagTypeEnum theTagType,
-			String theScheme,
-			String theTerm,
-			String theLabel,
-			String theVersion,
-			Boolean theUserSelected) {
-
-		TypedQuery<TagDefinition> q = buildTagQuery(theTagType, theScheme, theTerm, theVersion, theUserSelected);
-		q.setMaxResults(1);
-
-		TransactionTemplate template = new TransactionTemplate(myTransactionManager);
-		template.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
-
-		// this transaction will attempt to get or create the tag,
-		// repeating (on any failure) 10 times.
-		// if it fails more than this, we will throw exceptions
-		TagDefinition retVal;
-		int count = 0;
-		HashSet<Throwable> throwables = new HashSet<>();
-		do {
-			try {
-				retVal = template.execute(new TransactionCallback<TagDefinition>() {
-
-					// do the actual DB call(s) to read and/or write the values
-					private TagDefinition readOrCreate() {
-						TagDefinition val;
-						try {
-							val = q.getSingleResult();
-						} catch (NoResultException e) {
-							val = new TagDefinition(theTagType, theScheme, theTerm, theLabel);
-							val.setVersion(theVersion);
-							val.setUserSelected(theUserSelected);
-							myEntityManager.persist(val);
-						}
-						return val;
-					}
-
-					@Override
-					public TagDefinition doInTransaction(TransactionStatus status) {
-						TagDefinition tag = null;
-
-						try {
-							tag = readOrCreate();
-						} catch (Exception ex) {
-							// log any exceptions - just in case
-							// they may be signs of things to come...
-							ourLog.warn(
-									"Tag read/write failed: "
-											+ ex.getMessage() + ". "
-											+ "This is not a failure on its own, "
-											+ "but could be useful information in the result of an actual failure.",
-									ex);
-							throwables.add(ex);
-						}
-
-						return tag;
-					}
-				});
-			} catch (Exception ex) {
-				// transaction template can fail if connections to db are exhausted and/or timeout
-				ourLog.warn(
-						"Transaction failed with: {}. Transaction will rollback and be reattempted.", ex.getMessage());
-				retVal = null;
-			}
-			count++;
-		} while (retVal == null && count < TOTAL_TAG_READ_ATTEMPTS);
-
-		if (retVal == null) {
-			// if tag is still null,
-			// something bad must be happening
-			// - throw
-			String msg = throwables.stream().map(Throwable::getMessage).collect(Collectors.joining(", "));
-			throw new InternalErrorException(Msg.code(2023)
-					+ "Tag get/create failed after "
-					+ TOTAL_TAG_READ_ATTEMPTS
-					+ " attempts with error(s): "
-					+ msg);
-		}
-
-		return retVal;
-	}
-
-	private TypedQuery<TagDefinition> buildTagQuery(
-			TagTypeEnum theTagType, String theScheme, String theTerm, String theVersion, Boolean theUserSelected) {
-		CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
-		CriteriaQuery<TagDefinition> cq = builder.createQuery(TagDefinition.class);
-		Root<TagDefinition> from = cq.from(TagDefinition.class);
-
-		List<Predicate> predicates = new ArrayList<>();
-		predicates.add(builder.and(
-				builder.equal(from.get("myTagType"), theTagType), builder.equal(from.get("myCode"), theTerm)));
-
-		predicates.add(
-				isBlank(theScheme)
-						? builder.isNull(from.get("mySystem"))
-						: builder.equal(from.get("mySystem"), theScheme));
-
-		predicates.add(
-				isBlank(theVersion)
-						? builder.isNull(from.get("myVersion"))
-						: builder.equal(from.get("myVersion"), theVersion));
-
-		predicates.add(
-				isNull(theUserSelected)
-						? builder.isNull(from.get("myUserSelected"))
-						: builder.equal(from.get("myUserSelected"), theUserSelected));
-
-		cq.where(predicates.toArray(new Predicate[0]));
-		return myEntityManager.createQuery(cq);
-	}
-
 	void incrementId(T theResource, ResourceTable theSavedEntity, IIdType theResourceId) {
 		if (theResourceId == null || theResourceId.getVersionIdPart() == null) {
 			theSavedEntity.initializeVersion();
@@ -933,7 +753,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 	@Override
 	@CoverageIgnore
 	public BaseHasResource readEntity(IIdType theValueId, RequestDetails theRequest) {
-		throw new NotImplementedException(Msg.code(927) + "");
+		throw new NotImplementedException(Msg.code(927));
 	}
 
 	/**
@@ -1839,9 +1659,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 	}
 
 	@PostConstruct
-	public void start() {
+	public void start() {}
-		// nothing yet
-	}
 
 	@VisibleForTesting
 	public void setStorageSettingsForUnitTest(JpaStorageSettings theStorageSettings) {
@@ -1880,30 +1698,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		myJpaStorageResourceParser = theJpaStorageResourceParser;
 	}
 
-	private class AddTagDefinitionToCacheAfterCommitSynchronization implements TransactionSynchronization {
-
-		private final TagDefinition myTagDefinition;
-		private final MemoryCacheService.TagDefinitionCacheKey myKey;
-
-		public AddTagDefinitionToCacheAfterCommitSynchronization(
-				MemoryCacheService.TagDefinitionCacheKey theKey, TagDefinition theTagDefinition) {
-			myTagDefinition = theTagDefinition;
-			myKey = theKey;
-		}
-
-		@Override
-		public void afterCommit() {
-			myMemoryCacheService.put(MemoryCacheService.CacheEnum.TAG_DEFINITION, myKey, myTagDefinition);
-		}
-	}
-
-	@Nonnull
-	public static MemoryCacheService.TagDefinitionCacheKey toTagDefinitionMemoryCacheKey(
-			TagTypeEnum theTagType, String theScheme, String theTerm, String theVersion, Boolean theUserSelected) {
-		return new MemoryCacheService.TagDefinitionCacheKey(
-				theTagType, theScheme, theTerm, theVersion, theUserSelected);
-	}
-
 	@SuppressWarnings("unchecked")
 	public static String parseContentTextIntoWords(FhirContext theContext, IBaseResource theResource) {
 

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

@@ -21,7 +21,6 @@ package ca.uhn.fhir.jpa.dao;
 
 import ca.uhn.fhir.batch2.api.IJobCoordinator;
 import ca.uhn.fhir.batch2.api.IJobPartitionProvider;
-import ca.uhn.fhir.batch2.jobs.reindex.ReindexAppCtx;
 import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
 import ca.uhn.fhir.batch2.model.JobInstanceStartRequest;
 import ca.uhn.fhir.context.FhirVersionEnum;
@@ -158,6 +157,7 @@ import java.util.function.Supplier;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
+import static ca.uhn.fhir.batch2.jobs.reindex.ReindexUtils.JOB_REINDEX;
 import static java.util.Objects.isNull;
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
@@ -1043,7 +1043,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			if (!entityHasTag) {
 				theEntity.setHasTags(true);
 
-				TagDefinition def = getTagOrNull(
+				TagDefinition def = cacheTagDefinitionDao.getTagOrNull(
 						theTransactionDetails,
 						nextDef.getTagType(),
 						nextDef.getSystem(),
@@ -1315,7 +1315,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			myJobPartitionProvider.getPartitionedUrls(theRequestDetails, urls).forEach(params::addPartitionedUrl);
 
 			JobInstanceStartRequest request = new JobInstanceStartRequest();
-			request.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
+			request.setJobDefinitionId(JOB_REINDEX);
 			request.setParameters(params);
 			myJobCoordinator.startInstance(theRequestDetails, request);
 

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

@@ -0,0 +1,132 @@
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2024 Smile CDR, Inc.
+ * %%
+ * 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%
+ */
+package ca.uhn.fhir.jpa.dao;
+
+import ca.uhn.fhir.jpa.dao.data.ITagDefinitionDao;
+import ca.uhn.fhir.jpa.model.entity.TagDefinition;
+import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
+import ca.uhn.fhir.jpa.util.MemoryCacheService;
+import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
+import jakarta.annotation.Nonnull;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.data.domain.Pageable;
+import org.springframework.stereotype.Repository;
+import org.springframework.transaction.support.TransactionSynchronization;
+import org.springframework.transaction.support.TransactionSynchronizationManager;
+
+import java.util.HashMap;
+import java.util.List;
+
+import static org.apache.commons.lang3.StringUtils.isBlank;
+
+@Repository
+public class CacheTagDefinitionDao {
+	private static final Logger ourLog = LoggerFactory.getLogger(CacheTagDefinitionDao.class);
+
+	private final ITagDefinitionDao tagDefinitionDao;
+	private final MemoryCacheService memoryCacheService;
+
+	public CacheTagDefinitionDao(ITagDefinitionDao tagDefinitionDao, MemoryCacheService memoryCacheService) {
+		this.tagDefinitionDao = tagDefinitionDao;
+		this.memoryCacheService = memoryCacheService;
+	}
+
+	/**
+	 * Returns a TagDefinition or null if the scheme, term, and label are all blank.
+	 */
+	protected TagDefinition getTagOrNull(
+			TransactionDetails transactionDetails,
+			TagTypeEnum tagType,
+			String scheme,
+			String term,
+			String label,
+			String version,
+			Boolean userSelected) {
+
+		if (isBlank(scheme) && isBlank(term) && isBlank(label)) {
+			return null;
+		}
+
+		MemoryCacheService.TagDefinitionCacheKey key =
+				toTagDefinitionMemoryCacheKey(tagType, scheme, term, version, userSelected);
+		TagDefinition tagDefinition = memoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.TAG_DEFINITION, key);
+
+		if (tagDefinition == null) {
+			HashMap<MemoryCacheService.TagDefinitionCacheKey, TagDefinition> resolvedTagDefinitions =
+					transactionDetails.getOrCreateUserData("resolvedTagDefinitions", HashMap::new);
+
+			tagDefinition = resolvedTagDefinitions.get(key);
+
+			if (tagDefinition == null) {
+				tagDefinition = getOrCreateTag(tagType, scheme, term, label, version, userSelected);
+
+				TransactionSynchronization sync =
+						new AddTagDefinitionToCacheAfterCommitSynchronization(key, tagDefinition);
+				TransactionSynchronizationManager.registerSynchronization(sync);
+
+				resolvedTagDefinitions.put(key, tagDefinition);
+			}
+		}
+
+		return tagDefinition;
+	}
+
+	/**
+	 * Gets or creates a TagDefinition entity.
+	 */
+	private TagDefinition getOrCreateTag(
+			TagTypeEnum tagType, String scheme, String term, String label, String version, Boolean userSelected) {
+		List<TagDefinition> result = tagDefinitionDao.findByTagTypeAndSchemeAndTermAndVersionAndUserSelected(
+				tagType, scheme, term, version, userSelected, Pageable.ofSize(1));
+
+		if (!result.isEmpty()) {
+			return result.get(0);
+		} else {
+			// Create a new TagDefinition if no result is found
+			TagDefinition newTag = new TagDefinition(tagType, scheme, term, label);
+			newTag.setVersion(version);
+			newTag.setUserSelected(userSelected);
+			return tagDefinitionDao.save(newTag);
+		}
+	}
+
+	@Nonnull
+	private static MemoryCacheService.TagDefinitionCacheKey toTagDefinitionMemoryCacheKey(
+			TagTypeEnum tagType, String scheme, String term, String version, Boolean userSelected) {
+		return new MemoryCacheService.TagDefinitionCacheKey(tagType, scheme, term, version, userSelected);
+	}
+
+	private class AddTagDefinitionToCacheAfterCommitSynchronization implements TransactionSynchronization {
+		private final TagDefinition tagDefinition;
+		private final MemoryCacheService.TagDefinitionCacheKey key;
+
+		public AddTagDefinitionToCacheAfterCommitSynchronization(
+				MemoryCacheService.TagDefinitionCacheKey key, TagDefinition tagDefinition) {
+			this.tagDefinition = tagDefinition;
+			this.key = key;
+		}
+
+		@Override
+		public void afterCommit() {
+			memoryCacheService.put(MemoryCacheService.CacheEnum.TAG_DEFINITION, key, tagDefinition);
+		}
+	}
+}

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

@@ -137,7 +137,8 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
 	public ExtendedHSearchIndexData extractLuceneIndexData(
 			IBaseResource theResource, ResourceIndexedSearchParams theNewParams) {
 		String resourceType = myFhirContext.getResourceType(theResource);
-		ResourceSearchParams activeSearchParams = mySearchParamRegistry.getActiveSearchParams(resourceType);
+		ResourceSearchParams activeSearchParams = mySearchParamRegistry.getActiveSearchParams(
+				resourceType, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
 		ExtendedHSearchIndexExtractor extractor = new ExtendedHSearchIndexExtractor(
 				myStorageSettings, myFhirContext, activeSearchParams, mySearchParamExtractor);
 		return extractor.extract(theResource, theNewParams);

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

@@ -27,7 +27,11 @@ import ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult;
 import ca.uhn.fhir.context.support.LookupCodeRequest;
 import ca.uhn.fhir.context.support.ValidationSupportContext;
 import ca.uhn.fhir.i18n.Msg;
+import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
+import ca.uhn.fhir.jpa.api.dao.ReindexOutcome;
+import ca.uhn.fhir.jpa.api.dao.ReindexParameters;
+import ca.uhn.fhir.jpa.api.model.ReindexJobStatus;
 import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
 import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
@@ -176,6 +180,47 @@ public class JpaResourceDaoCodeSystem<T extends IBaseResource> extends BaseHapiF
 		myTermDeferredStorageSvc.deleteCodeSystemForResource(theEntityToDelete);
 	}
 
+	/**
+	 * If there are more code systems to process
+	 * than {@link JpaStorageSettings#getDeferIndexingForCodesystemsOfSize()},
+	 * then these codes will have their processing deferred (for a later time).
+	 *
+	 * This can result in future reindex steps *skipping* these code systems (if
+	 * they're still deferred) and thus incorrect expansions resulting.
+	 *
+	 * So we override the reindex method for CodeSystems specifically to
+	 * force reindex batch jobs to wait until all code systems are processed before
+	 * moving on.
+	 */
+	@SuppressWarnings("rawtypes")
+	@Override
+	public ReindexOutcome reindex(
+			IResourcePersistentId thePid,
+			ReindexParameters theReindexParameters,
+			RequestDetails theRequest,
+			TransactionDetails theTransactionDetails) {
+		ReindexOutcome outcome = super.reindex(thePid, theReindexParameters, theRequest, theTransactionDetails);
+
+		if (outcome.getWarnings().isEmpty()) {
+			outcome.setHasPendingWork(true);
+		}
+		return outcome;
+	}
+
+	@Override
+	public ReindexJobStatus getReindexJobStatus() {
+		boolean isQueueEmpty = myTermDeferredStorageSvc.isStorageQueueEmpty(true);
+
+		ReindexJobStatus status = new ReindexJobStatus();
+		status.setHasReindexWorkPending(!isQueueEmpty);
+		if (status.isHasReindexWorkPending()) {
+			// force a run
+			myTermDeferredStorageSvc.saveDeferred();
+		}
+
+		return status;
+	}
+
 	@Override
 	public ResourceTable updateEntity(
 			RequestDetails theRequest,

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IBatch2JobInstanceRepository.java

@@ -19,6 +19,7 @@
  */
 package ca.uhn.fhir.jpa.dao.data;
 
+import ca.uhn.fhir.batch2.model.BatchInstanceStatusDTO;
 import ca.uhn.fhir.batch2.model.StatusEnum;
 import ca.uhn.fhir.jpa.entity.Batch2JobInstanceEntity;
 import org.springframework.data.domain.Pageable;
@@ -91,4 +92,8 @@ public interface IBatch2JobInstanceRepository
 	@Query("SELECT e FROM Batch2JobInstanceEntity e WHERE e.myDefinitionId = :jobDefinitionId")
 	List<Batch2JobInstanceEntity> findInstancesByJobDefinitionId(
 			@Param("jobDefinitionId") String theJobDefinitionId, Pageable thePageRequest);
+
+	@Query(
+			"SELECT new ca.uhn.fhir.batch2.model.BatchInstanceStatusDTO(e.myId, e.myStatus, e.myStartTime, e.myEndTime) FROM Batch2JobInstanceEntity e WHERE e.myId = :id")
+	BatchInstanceStatusDTO fetchBatchInstanceStatus(@Param("id") String theInstanceId);
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IBatch2WorkChunkRepository.java

@@ -19,6 +19,7 @@
  */
 package ca.uhn.fhir.jpa.dao.data;
 
+import ca.uhn.fhir.batch2.model.BatchWorkChunkStatusDTO;
 import ca.uhn.fhir.batch2.model.WorkChunkStatusEnum;
 import ca.uhn.fhir.jpa.entity.Batch2WorkChunkEntity;
 import org.springframework.data.domain.Pageable;
@@ -147,4 +148,8 @@ public interface IBatch2WorkChunkRepository
 			@Param("instanceId") String theInstanceId,
 			@Param("stepId") String theStepId,
 			@Param("status") WorkChunkStatusEnum theStatus);
+
+	@Query(
+			"SELECT new ca.uhn.fhir.batch2.model.BatchWorkChunkStatusDTO(e.myTargetStepId, e.myStatus, min(e.myStartTime), max(e.myEndTime), avg(e.myEndTime - e.myStartTime), count(*)) FROM Batch2WorkChunkEntity e WHERE e.myInstanceId=:instanceId GROUP BY e.myTargetStepId, e.myStatus")
+	List<BatchWorkChunkStatusDTO> fetchWorkChunkStatusForInstance(@Param("instanceId") String theInstanceId);
 }

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

@@ -20,8 +20,25 @@
 package ca.uhn.fhir.jpa.dao.data;
 
 import ca.uhn.fhir.jpa.model.entity.TagDefinition;
+import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
+import org.springframework.data.domain.Pageable;
 import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.query.Param;
+
+import java.util.List;
 
 public interface ITagDefinitionDao extends JpaRepository<TagDefinition, Long>, IHapiFhirJpaRepository {
-	// nothing
+	@Query("SELECT t FROM TagDefinition t WHERE " + "t.myTagType = :tagType AND "
+			+ "( :scheme IS NULL OR :scheme = '' OR t.mySystem = :scheme ) AND "
+			+ "t.myCode = :term AND "
+			+ "( :version IS NULL OR :version = '' OR t.myVersion = :version ) AND "
+			+ "( :userSelected IS NULL OR t.myUserSelected = :userSelected )")
+	List<TagDefinition> findByTagTypeAndSchemeAndTermAndVersionAndUserSelected(
+			@Param("tagType") TagTypeEnum tagType,
+			@Param("scheme") String scheme,
+			@Param("term") String term,
+			@Param("version") String version,
+			@Param("userSelected") Boolean userSelected,
+			Pageable pageable);
 }

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

@@ -92,7 +92,8 @@ public class ExtendedHSearchSearchBuilder {
 			String theResourceType, SearchParameterMap myParams, ISearchParamRegistry theSearchParamRegistry) {
 		boolean canUseHibernate = false;
 
-		ResourceSearchParams resourceActiveSearchParams = theSearchParamRegistry.getActiveSearchParams(theResourceType);
+		ResourceSearchParams resourceActiveSearchParams = theSearchParamRegistry.getActiveSearchParams(
+				theResourceType, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
 		for (String paramName : myParams.keySet()) {
 			// is this parameter supported?
 			if (illegalForHibernateSearch(paramName, resourceActiveSearchParams)) {
@@ -218,7 +219,8 @@ public class ExtendedHSearchSearchBuilder {
 
 		// copy the keys to avoid concurrent modification error
 		ArrayList<String> paramNames = compileParamNames(searchParameterMap);
-		ResourceSearchParams activeSearchParams = searchParamRegistry.getActiveSearchParams(resourceType);
+		ResourceSearchParams activeSearchParams = searchParamRegistry.getActiveSearchParams(
+				resourceType, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
 		for (String nextParam : paramNames) {
 			if (illegalForHibernateSearch(nextParam, activeSearchParams)) {
 				// ignore magic params handled in JPA

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

@@ -151,7 +151,8 @@ public class HSearchSortHelperImpl implements IHSearchSortHelper {
 	 */
 	@VisibleForTesting
 	Optional<RestSearchParameterTypeEnum> getParamType(String theResourceTypeName, String theParamName) {
-		ResourceSearchParams activeSearchParams = mySearchParamRegistry.getActiveSearchParams(theResourceTypeName);
+		ResourceSearchParams activeSearchParams = mySearchParamRegistry.getActiveSearchParams(
+				theResourceTypeName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
 		RuntimeSearchParam searchParam = activeSearchParams.get(theParamName);
 		if (searchParam == null) {
 			return Optional.empty();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/graphql/GraphQLProviderWithIntrospection.java

@@ -181,7 +181,8 @@ public class GraphQLProviderWithIntrospection extends GraphQLProvider {
 			for (String nextResourceType : theResourceTypes) {
 				StructureDefinition sd = fetchStructureDefinition(nextResourceType);
 				List<SearchParameter> parameters = toR5SearchParams(mySearchParamRegistry
-						.getActiveSearchParams(nextResourceType)
+						.getActiveSearchParams(
+								nextResourceType, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH)
 						.values());
 				myGenerator.generateResource(writer, sd, parameters, theOperations);
 			}
@@ -198,7 +199,8 @@ public class GraphQLProviderWithIntrospection extends GraphQLProvider {
 				}
 				if (theOperations.contains(GraphQLSchemaGenerator.FHIROperationType.SEARCH)) {
 					List<SearchParameter> parameters = toR5SearchParams(mySearchParamRegistry
-							.getActiveSearchParams(nextResourceType)
+							.getActiveSearchParams(
+									nextResourceType, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH)
 							.values());
 					myGenerator.generateListAccessQuery(writer, parameters, nextResourceType);
 					myGenerator.generateConnectionAccessQuery(writer, parameters, nextResourceType);