Ks 20211209 xml to java (#3236)

* try xml -> json

* Change from xml serialization to json serialization.  Also fix a deadlock in how the validation cache is used.

* changelog

* back out logback
change

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3236-change-validation-from-xml-to-java.yaml

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

Co-authored-by: Tadgh <tadgh@cs.toronto.edu>

hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/ValidationContext.java

@@ -96,12 +96,12 @@ public class ValidationContext<T> extends BaseValidationContext<T> implements IV
 		IEncoder encoder = new IEncoder() {
 			@Override
 			public String encode() {
-				return theContext.newXmlParser().encodeResourceToString(theResource);
+				return theContext.newJsonParser().encodeResourceToString(theResource);
 			}
 
 			@Override
 			public EncodingEnum getEncoding() {
-				return EncodingEnum.XML;
+				return EncodingEnum.JSON;
 			}
 		};
 		return new ValidationContext<>(theContext, theResource, encoder, options);

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3236-change-validation-from-xml-to-java.yaml

@@ -0,0 +1,3 @@
+---
+type: perf
+title: "Improved validation performance by switching validation serialization from XML to JSON."

hapi-fhir-jpaserver-base/src/test/resources/r4/code-in-unknown-system-with-required-binding.xml

@@ -22,7 +22,6 @@
 			<code value="encounter-diagnosis"/>
 			<display value="Encounter Diagnosis"/>
 		</coding>
-		<!--   and also a SNOMED CT coding   -->
 		<coding>
 			<system value="http://snomed.info/sct"/>
 			<code value="439401001"/>

hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/CachingValidationSupport.java

@@ -141,7 +141,7 @@ public class CachingValidationSupport extends BaseValidationSupportWrapper imple
 	@Override
 	public boolean isCodeSystemSupported(ValidationSupportContext theValidationSupportContext, String theSystem) {
 		String key = "isCodeSystemSupported " + theSystem;
-		Boolean retVal = loadFromCache(myCache, key, t -> super.isCodeSystemSupported(theValidationSupportContext, theSystem));
+		Boolean retVal = loadFromCacheReentrantSafe(myCache, key, t -> super.isCodeSystemSupported(theValidationSupportContext, theSystem));
 		assert retVal != null;
 		return retVal;
 	}
@@ -188,6 +188,27 @@ public class CachingValidationSupport extends BaseValidationSupportWrapper imple
 		return result.orElse(null);
 	}
 
+	/**
+	 * The Caffeine cache uses ConcurrentHashMap which is not reentrant, so if we get unlucky and the hashtable
+	 * needs to grow at the same time as we are in a reentrant cache lookup, the thread will deadlock.  Use this
+	 * method in place of loadFromCache in situations where a cache lookup calls another cache lookup within its lambda
+	 */
+	@Nullable
+	private <S, T> T loadFromCacheReentrantSafe(Cache<S, Object> theCache, S theKey, Function<S, T> theLoader) {
+		ourLog.trace("Reentrant fetch from cache: {}", theKey);
+
+		Optional<T> result = (Optional<T>) theCache.getIfPresent(theKey);
+		if (result != null && result.isPresent()) {
+			return result.get();
+		}
+		T value = theLoader.apply(theKey);
+		assert value != null;
+
+		theCache.put(theKey, Optional.of(value));
+
+		return value;
+	}
+
 	private <S, T> T loadFromCacheWithAsyncRefresh(Cache<S, Object> theCache, S theKey, Function<S, T> theLoader) {
 		T retVal = (T) theCache.getIfPresent(theKey);
 		if (retVal == null) {