Merge branch 'hapifhir:master' into fix/remove-entity-embeddable-conf…

…lict

hapi-deployable-pom/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		 <groupId>ca.uhn.hapi.fhir</groupId>
 		 <artifactId>hapi-fhir</artifactId>
-		 <version>7.7.14-SNAPSHOT</version>
+		 <version>7.7.16-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>7.7.14-SNAPSHOT</version>
+		<version>7.7.16-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>7.7.14-SNAPSHOT</version>
+		<version>7.7.16-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-base/src/main/java/ca/uhn/fhir/narrative2/INarrativeTemplate.java

@@ -28,6 +28,8 @@ public interface INarrativeTemplate {
 
 	Set<String> getAppliesToProfiles();
 
+	Set<String> getAppliesToCode();
+
 	Set<String> getAppliesToResourceTypes();
 
 	Set<Class<? extends IBase>> getAppliesToClasses();

hapi-fhir-base/src/main/java/ca/uhn/fhir/narrative2/INarrativeTemplateManifest.java

@@ -32,7 +32,8 @@ List<INarrativeTemplate> getTemplateByResourceName(
 			@Nonnull FhirContext theFhirContext,
 			@Nonnull EnumSet<TemplateTypeEnum> theStyles,
 			@Nonnull String theResourceName,
-			@Nonnull Collection<String> theProfiles);
+			@Nonnull Collection<String> theProfiles,
+			@Nonnull Collection<String> theCodes);
 
 	List<INarrativeTemplate> getTemplateByName(
 			@Nonnull FhirContext theFhirContext, @Nonnull EnumSet<TemplateTypeEnum> theStyles, @Nonnull String theName);

hapi-fhir-base/src/main/java/ca/uhn/fhir/narrative2/NarrativeTemplate.java

@@ -34,6 +34,7 @@ public class NarrativeTemplate implements INarrativeTemplate {
 	private final Set<String> myAppliesToDataTypes = new HashSet<>();
 	private final Set<Class<? extends IBase>> myAppliesToClasses = new HashSet<>();
 	private final Set<String> myAppliesToFragmentNames = new HashSet<>();
+	private final Set<String> myAppliesToCode = new HashSet<>();
 	private String myTemplateFileName;
 	private TemplateTypeEnum myTemplateType = TemplateTypeEnum.THYMELEAF;
 	private String myContextPath;
@@ -81,10 +82,19 @@ public Set<String> getAppliesToProfiles() {
 		return Collections.unmodifiableSet(myAppliesToProfiles);
 	}
 
+	@Override
+	public Set<String> getAppliesToCode() {
+		return Collections.unmodifiableSet(myAppliesToCode);
+	}
+
 	void addAppliesToProfile(String theAppliesToProfile) {
 		myAppliesToProfiles.add(theAppliesToProfile);
 	}
 
+	void addAppliesToCode(String theAppliesToCode) {
+		myAppliesToCode.add(theAppliesToCode);
+	}
+
 	@Override
 	public Set<String> getAppliesToResourceTypes() {
 		return Collections.unmodifiableSet(myAppliesToResourceTypes);

hapi-fhir-base/src/main/java/ca/uhn/fhir/narrative2/NarrativeTemplateManifest.java

@@ -107,24 +107,25 @@ public List<INarrativeTemplate> getTemplateByResourceName(
 			@Nonnull FhirContext theFhirContext,
 			@Nonnull EnumSet<TemplateTypeEnum> theStyles,
 			@Nonnull String theResourceName,
-			@Nonnull Collection<String> theProfiles) {
-		return getFromMap(theStyles, theResourceName.toUpperCase(), myResourceTypeToTemplate, theProfiles);
+			@Nonnull Collection<String> theProfiles,
+			@Nonnull Collection<String> theCodes) {
+		return getFromMap(theStyles, theResourceName.toUpperCase(), myResourceTypeToTemplate, theProfiles, theCodes);
 	}
 
 	@Override
 	public List<INarrativeTemplate> getTemplateByName(
 			@Nonnull FhirContext theFhirContext,
 			@Nonnull EnumSet<TemplateTypeEnum> theStyles,
 			@Nonnull String theName) {
-		return getFromMap(theStyles, theName, myNameToTemplate, Collections.emptyList());
+		return getFromMap(theStyles, theName, myNameToTemplate);
 	}
 
 	@Override
 	public List<INarrativeTemplate> getTemplateByFragmentName(
 			@Nonnull FhirContext theFhirContext,
 			@Nonnull EnumSet<TemplateTypeEnum> theStyles,
 			@Nonnull String theFragmentName) {
-		return getFromMap(theStyles, theFragmentName, myFragmentNameToTemplate, Collections.emptyList());
+		return getFromMap(theStyles, theFragmentName, myFragmentNameToTemplate);
 	}
 
 	@SuppressWarnings("PatternVariableCanBeUsed")
@@ -138,22 +139,30 @@ public List<INarrativeTemplate> getTemplateByElement(
 		if (theElement instanceof IBaseResource) {
 			IBaseResource resource = (IBaseResource) theElement;
 			String resourceName = theFhirContext.getResourceDefinition(resource).getName();
+
 			List<String> profiles = resource.getMeta().getProfile().stream()
 					.filter(Objects::nonNull)
 					.map(IPrimitiveType::getValueAsString)
 					.filter(StringUtils::isNotBlank)
 					.collect(Collectors.toList());
-			retVal = getTemplateByResourceName(theFhirContext, theStyles, resourceName, profiles);
+
+			List<String> codes = resource.getMeta().getTag().stream()
+					.filter(Objects::nonNull)
+					.filter(f -> StringUtils.isNotBlank(f.getSystem()) && StringUtils.isNotBlank(f.getCode()))
+					.map(t -> t.getSystem() + "|" + t.getCode())
+					.collect(Collectors.toList());
+
+			retVal = getTemplateByResourceName(theFhirContext, theStyles, resourceName, profiles, codes);
 		}
 
 		if (retVal.isEmpty()) {
-			retVal = getFromMap(theStyles, theElement.getClass().getName(), myClassToTemplate, Collections.emptyList());
+			retVal = getFromMap(theStyles, theElement.getClass().getName(), myClassToTemplate);
 		}
 
 		if (retVal.isEmpty()) {
 			String datatypeName =
 					theFhirContext.getElementDefinition(theElement.getClass()).getName();
-			retVal = getFromMap(theStyles, datatypeName.toUpperCase(), myDatatypeToTemplate, Collections.emptyList());
+			retVal = getFromMap(theStyles, datatypeName.toUpperCase(), myDatatypeToTemplate);
 		}
 		return retVal;
 	}
@@ -222,6 +231,11 @@ private static Collection<NarrativeTemplate> loadProperties(String theManifestTe
 				if (isNotBlank(profile)) {
 					nextTemplate.addAppliesToProfile(profile);
 				}
+			} else if (nextKey.endsWith(".tag")) {
+				String tag = file.getProperty(nextKey);
+				if (isNotBlank(tag)) {
+					nextTemplate.addAppliesToCode(tag);
+				}
 			} else if (nextKey.endsWith(".resourceType")) {
 				String resourceType = file.getProperty(nextKey);
 				parseValuesAndAddToMap(resourceType, nextTemplate::addAppliesToResourceType);
@@ -282,15 +296,22 @@ static String loadResource(String theName) {
 		}
 	}
 
+	private static <T> List<INarrativeTemplate> getFromMap(
+			EnumSet<TemplateTypeEnum> theStyles, T theKey, ListMultimap<T, NarrativeTemplate> theMap) {
+		return getFromMap(theStyles, theKey, theMap, Collections.emptyList(), Collections.emptyList());
+	}
+
 	private static <T> List<INarrativeTemplate> getFromMap(
 			EnumSet<TemplateTypeEnum> theStyles,
 			T theKey,
 			ListMultimap<T, NarrativeTemplate> theMap,
-			Collection<String> theProfiles) {
+			Collection<String> theProfiles,
+			Collection<String> theCodes) {
 		return theMap.get(theKey).stream()
 				.filter(t -> theStyles.contains(t.getTemplateType()))
 				.filter(t -> theProfiles.isEmpty()
 						|| t.getAppliesToProfiles().stream().anyMatch(theProfiles::contains))
+				.filter(t -> theCodes.isEmpty() || t.getAppliesToCode().stream().anyMatch(theCodes::contains))
 				.collect(Collectors.toList());
 	}
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/system/HapiSystemProperties.java

@@ -19,23 +19,22 @@
  */
 package ca.uhn.fhir.system;
 
-import org.apache.commons.lang3.time.DateUtils;
+import java.util.concurrent.TimeUnit;
 
 public final class HapiSystemProperties {
 	static final String SUPPRESS_HAPI_FHIR_VERSION_LOG = "suppress_hapi_fhir_version_log";
 	static final String DISABLE_STATUS_BASED_REINDEX = "disable_status_based_reindex";
 	/**
 	 * This is provided for testing only! Use with caution as this property may change.
 	 */
-	static final String TEST_SYSTEM_PROP_VALIDATION_RESOURCE_CACHES_MS =
-			"TEST_SYSTEM_PROP_VALIDATION_RESOURCE_CACHES_MS";
+	static final String VALIDATION_RESOURCE_CACHE_TIMEOUT_MILLIS = "VALIDATION_RESOURCE_CACHE_EXPIRY_MS";
 
 	static final String UNIT_TEST_CAPTURE_STACK = "unit_test_capture_stack";
 	static final String STACKFILTER_PATTERN_PROP = "log.stackfilter.pattern";
 	static final String HAPI_CLIENT_KEEPRESPONSES = "hapi.client.keepresponses";
 	static final String TEST_MODE = "test";
 	static final String UNIT_TEST_MODE = "unit_test_mode";
-	static final long DEFAULT_TEST_SYSTEM_PROP_VALIDATION_RESOURCE_CACHES_MS = 10 * DateUtils.MILLIS_PER_SECOND;
+	static final long DEFAULT_VALIDATION_RESOURCE_CACHE_TIMEOUT_MILLIS = TimeUnit.MINUTES.toMillis(10);
 	static final String PREVENT_INVALIDATING_CONDITIONAL_MATCH_CRITERIA =
 			"hapi.storage.prevent_invalidating_conditional_match_criteria";
 
@@ -75,20 +74,20 @@ public static void setStackFilterPattern(String thePattern) {
 	/**
 	 * Set the validation resource cache expireAfterWrite timeout in milliseconds
 	 *
-	 * @param theMillis
+	 * @param theMillis the timeout value to set (in milliseconds)
 	 */
-	public static void setTestValidationResourceCachesMs(long theMillis) {
-		System.setProperty(TEST_SYSTEM_PROP_VALIDATION_RESOURCE_CACHES_MS, "" + theMillis);
+	public static void setValidationResourceCacheTimeoutMillis(long theMillis) {
+		System.setProperty(VALIDATION_RESOURCE_CACHE_TIMEOUT_MILLIS, "" + theMillis);
 	}
 
 	/**
 	 * Get the validation resource cache expireAfterWrite timeout in milliseconds.  If it has not been set, the default
 	 * value is 10 seconds.
 	 */
-	public static long getTestValidationResourceCachesMs() {
-		String property = System.getProperty(TEST_SYSTEM_PROP_VALIDATION_RESOURCE_CACHES_MS);
+	public static long getValidationResourceCacheTimeoutMillis() {
+		String property = System.getProperty(VALIDATION_RESOURCE_CACHE_TIMEOUT_MILLIS);
 		if (property == null) {
-			return DEFAULT_TEST_SYSTEM_PROP_VALIDATION_RESOURCE_CACHES_MS;
+			return DEFAULT_VALIDATION_RESOURCE_CACHE_TIMEOUT_MILLIS;
 		}
 		return Long.parseLong(property);
 	}

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

@@ -265,30 +265,48 @@ public static IBase addIssueWithMessageId(
 	}
 
 	public static void addDetailsToIssue(FhirContext theFhirContext, IBase theIssue, String theSystem, String theCode) {
+		addDetailsToIssue(theFhirContext, theIssue, theSystem, theCode, null);
+	}
+
+	public static void addDetailsToIssue(
+			FhirContext theFhirContext, IBase theIssue, String theSystem, String theCode, String theText) {
 		BaseRuntimeElementCompositeDefinition<?> issueElement =
 				(BaseRuntimeElementCompositeDefinition<?>) theFhirContext.getElementDefinition(theIssue.getClass());
 		BaseRuntimeChildDefinition detailsChildDef = issueElement.getChildByName("details");
-
-		BaseRuntimeElementCompositeDefinition<?> codingDef =
-				(BaseRuntimeElementCompositeDefinition<?>) theFhirContext.getElementDefinition("Coding");
-		ICompositeType coding = (ICompositeType) codingDef.newInstance();
-
-		// System
-		IPrimitiveType<?> system =
-				(IPrimitiveType<?>) theFhirContext.getElementDefinition("uri").newInstance();
-		system.setValueAsString(theSystem);
-		codingDef.getChildByName("system").getMutator().addValue(coding, system);
-
-		// Code
-		IPrimitiveType<?> code =
-				(IPrimitiveType<?>) theFhirContext.getElementDefinition("code").newInstance();
-		code.setValueAsString(theCode);
-		codingDef.getChildByName("code").getMutator().addValue(coding, code);
 		BaseRuntimeElementCompositeDefinition<?> ccDef =
 				(BaseRuntimeElementCompositeDefinition<?>) theFhirContext.getElementDefinition("CodeableConcept");
-
 		ICompositeType codeableConcept = (ICompositeType) ccDef.newInstance();
-		ccDef.getChildByName("coding").getMutator().addValue(codeableConcept, coding);
+
+		if (isNotBlank(theSystem) || isNotBlank(theCode)) {
+			BaseRuntimeElementCompositeDefinition<?> codingDef =
+					(BaseRuntimeElementCompositeDefinition<?>) theFhirContext.getElementDefinition("Coding");
+			ICompositeType coding = (ICompositeType) codingDef.newInstance();
+
+			// System
+			if (isNotBlank(theSystem)) {
+				IPrimitiveType<?> system = (IPrimitiveType<?>)
+						theFhirContext.getElementDefinition("uri").newInstance();
+				system.setValueAsString(theSystem);
+				codingDef.getChildByName("system").getMutator().addValue(coding, system);
+			}
+
+			// Code
+			if (isNotBlank(theCode)) {
+				IPrimitiveType<?> code = (IPrimitiveType<?>)
+						theFhirContext.getElementDefinition("code").newInstance();
+				code.setValueAsString(theCode);
+				codingDef.getChildByName("code").getMutator().addValue(coding, code);
+			}
+
+			ccDef.getChildByName("coding").getMutator().addValue(codeableConcept, coding);
+		}
+
+		if (isNotBlank(theText)) {
+			IPrimitiveType<?> textElem = (IPrimitiveType<?>)
+					ccDef.getChildByName("text").getChildByName("text").newInstance(theText);
+			ccDef.getChildByName("text").getMutator().addValue(codeableConcept, textElem);
+		}
+
 		detailsChildDef.getMutator().addValue(theIssue, codeableConcept);
 	}
 

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

@@ -0,0 +1,69 @@
+/*-
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * 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.util;
+
+import jakarta.annotation.Nonnull;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.concurrent.atomic.AtomicBoolean;
+import java.util.stream.Stream;
+
+/**
+ * This class collects items from a stream to a given limit and know whether there are
+ * still more items beyond that limit.
+ *
+ * @param <T> the type of object being streamed
+ */
+public class StopLimitAccumulator<T> {
+	private final boolean isTruncated;
+	private final List<T> myList;
+
+	private StopLimitAccumulator(List<T> theList, boolean theIsTruncated) {
+		myList = Collections.unmodifiableList(theList);
+		isTruncated = theIsTruncated;
+	}
+
+	public static <T> StopLimitAccumulator<T> fromStreamAndLimit(@Nonnull Stream<T> theItemStream, long theLimit) {
+		assert theLimit > 0;
+		AtomicBoolean isBeyondLimit = new AtomicBoolean(false);
+		List<T> accumulator = new ArrayList<>();
+
+		theItemStream
+				.limit(theLimit + 1) // Fetch one extra item to see if there are any more items past our limit
+				.forEach(item -> {
+					if (accumulator.size() < theLimit) {
+						accumulator.add(item);
+					} else {
+						isBeyondLimit.set(true);
+					}
+				});
+		return new StopLimitAccumulator<>(accumulator, isBeyondLimit.get());
+	}
+
+	public boolean isTruncated() {
+		return isTruncated;
+	}
+
+	public List<T> getItemList() {
+		return myList;
+	}
+}