7.6.0 Mergeback (#6494)

* 6323 resource creation deadlock (#6324) * make map reads concurrent * change log * CUstom version number for guaranteed build determinism * licenses * Expand translation cache (#6341) * Expand translation cache * Add changelog * Correction to #6341 (#6342) * Contained bug (#6402) * Contained bug * more tests * changelog, tests, implementation * code review * backwards logic * Fix Questionnaire doc (#6400) * fix reindex optimizeStorage=ALL_VERSIONS (#6421) * fixing broken rename of last step of reindex (#6429) * Fixes for the translation of parameter issues as part of the output for $validate-code operation. (#6438) * Move the validation providers to the test utilities package such that they can be reused. * Update IValidationSupport.CodeValidationIssue structure such that it meets the FHIR specification. Update RemoteTerminologyServiceValidationSupport and VersionSpecificWorkerContextWrapper translation for issues. * New tests for issue translation. Move test class to a different package so that we can add another test class. * Some simplification in the issue API to simplify building of issues. * Fix compilation errors. * Update providers to allow multiple responses and add support for the fetchCodeSystem call through method find. * Setup the first test for resource validation with remote terminology providers. * Fix NullPointerException * avoid calling validateCode for CodeSystem where system is null * Keep old public API methods (and class name) in IValidationSupport and mark them as deprecated to avoid breaking dependencies. * Revert local change to debug for duplicate errors. * Add more test cases for resource validation. Throw exception to signal missing test setup to make it obvious. * Simplify test setup. * Add some more javadoc * Add javadoc for the new test class * Add more tests * Address code review comments in IValidationSupport. * Add changelog * Change Repository search interface from Map to Multimap (#6445) Change Map to Multimap to support multiple and clauses. * licenses * fix interceptor hooks from requestDetails not getting called for STORAGE_PRECHECK_FOR_CACHED_SEARCH (#6436) * fix interceptor hooks from requestDetails not getting called for STORAGE_PRECHECK_FOR_CACHED_SEARCH * added unit tests and updated changelog * added one more test case * Add Adapter api (#6450) Lightweight implementation of the adapter pattern. * Bulk Import job status not changed after activation - failing test, fix, changelog (#6452) * Update CR to 3.13.1 (#6433) * Automated Migration Testing (HAPI-FHIR) - updated test migration scripts for 7_4_0 (#6439) * Rel 7 6 CVE (#6446) * Bump commons io * Bump HS and Lucene, and hibernate * Jetty bump for CVE * Resolve CVES * Bump with mismatch lucene * Bump velocity template engine * Revert bom bump * wip * Version bump * move changelog, fix cve * Bump commons-lang * Replace imports * wip * fix HQL break * remove dead code * Fix changelog entry * Bump org.hl7.fhir.core to 6.4.0 (#6454) * Bump HAPI version + org.hl7.fhir.core to 6.4.0 * Apply spotless * Correct a bug with duplicate parser IDs being assigned. (#6456) * Fix changelog entry * wip * compilation problem * Correct tests * changelog * Update hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/JsonParserR4Test.java Co-authored-by: volodymyr-korzh <[email protected]> * Correct a bug with duplicate parser IDs being assigned - test fixes * Correct a bug with duplicate parser IDs being assigned - spotless * Correct a bug with duplicate parser IDs being assigned - added test-utilities dependency to fhir-structures poms * Correct a bug with duplicate parser IDs being assigned - test fixes * Contained resources without assigned IDs are now assigned GUIDs - address comments --------- Co-authored-by: volodymyr-korzh <[email protected]> Co-authored-by: volodymyr <[email protected]> * licenses * ValueSet expansion fails if Hibernate Search configured to use Lucene - fixed incompatibility between Hibernate Search and Lucene versions (#6468) * Change the migrator to avoid table locks when adding an index. (#6489) * version bump * Updating version to: 7.6.1 post release. * Bump to 7.7.7. * deadsapce * Profile reference param (#6501) * updated QueryStack to not throw error with _profile as a ReferenceParam * update QueryStack * remove warnings * cleanup cast * cleanup test * add changelog * cleanup imports * updates per review feedback * updates per review feedback --------- Co-authored-by: [email protected] <[email protected]> * move changelog --------- Co-authored-by: JasonRoberts-smile <[email protected]> Co-authored-by: James Agnew <[email protected]> Co-authored-by: Brenin Rhodes <[email protected]> Co-authored-by: Emre Dincturk <[email protected]> Co-authored-by: TipzCM <[email protected]> Co-authored-by: Martha Mitran <[email protected]> Co-authored-by: Michael Buckley <[email protected]> Co-authored-by: volodymyr-korzh <[email protected]> Co-authored-by: dotasek <[email protected]> Co-authored-by: volodymyr <[email protected]> Co-authored-by: markiantorno <[email protected]> Co-authored-by: Gary Graham <[email protected]> Co-authored-by: Taha <[email protected]> Co-authored-by: [email protected] <[email protected]>
hapifhir · Nov 24, 2024 · 86c2c13 · 86c2c13
1 parent d4f1766
commit 86c2c13
Show file tree

Hide file tree

Showing 135 changed files with 3,794 additions and 1,041 deletions.
diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/IValidationSupport.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/IValidationSupport.java
diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java
@@ -105,7 +105,6 @@ public abstract class BaseParser implements IParser {
 	private static final Set<String> notEncodeForContainedResource =
 			new HashSet<>(Arrays.asList("security", "versionId", "lastUpdated"));
 
-	private FhirTerser.ContainedResources myContainedResources;
 	private boolean myEncodeElementsAppliesToChildResourcesOnly;
 	private final FhirContext myContext;
 	private Collection<String> myDontEncodeElements;
@@ -183,12 +182,15 @@ protected Iterable<CompositeChildElement> compositeChildIterator(
 	}
 
 	private String determineReferenceText(
-			IBaseReference theRef, CompositeChildElement theCompositeChildElement, IBaseResource theResource) {
+			IBaseReference theRef,
+			CompositeChildElement theCompositeChildElement,
+			IBaseResource theResource,
+			EncodeContext theContext) {
 		IIdType ref = theRef.getReferenceElement();
 		if (isBlank(ref.getIdPart())) {
 			String reference = ref.getValue();
 			if (theRef.getResource() != null) {
-				IIdType containedId = getContainedResources().getResourceId(theRef.getResource());
+				IIdType containedId = theContext.getContainedResources().getResourceId(theRef.getResource());
 				if (containedId != null && !containedId.isEmpty()) {
 					if (containedId.isLocal()) {
 						reference = containedId.getValue();
@@ -262,7 +264,8 @@ public String encodeResourceToString(IBaseResource theResource) throws DataForma
 	@Override
 	public final void encodeResourceToWriter(IBaseResource theResource, Writer theWriter)
 			throws IOException, DataFormatException {
-		EncodeContext encodeContext = new EncodeContext(this, myContext.getParserOptions());
+		EncodeContext encodeContext =
+				new EncodeContext(this, myContext.getParserOptions(), new FhirTerser.ContainedResources());
 		encodeResourceToWriter(theResource, theWriter, encodeContext);
 	}
 
@@ -285,7 +288,8 @@ public void encodeToWriter(IBase theElement, Writer theWriter) throws DataFormat
 		} else if (theElement instanceof IPrimitiveType) {
 			theWriter.write(((IPrimitiveType<?>) theElement).getValueAsString());
 		} else {
-			EncodeContext encodeContext = new EncodeContext(this, myContext.getParserOptions());
+			EncodeContext encodeContext =
+					new EncodeContext(this, myContext.getParserOptions(), new FhirTerser.ContainedResources());
 			encodeToWriter(theElement, theWriter, encodeContext);
 		}
 	}
@@ -404,10 +408,6 @@ protected String getCompositeElementId(IBase theElement) {
 		return elementId;
 	}
 
-	FhirTerser.ContainedResources getContainedResources() {
-		return myContainedResources;
-	}
-
 	@Override
 	public Set<String> getDontStripVersionsFromReferencesAtPaths() {
 		return myDontStripVersionsFromReferencesAtPaths;
@@ -539,10 +539,11 @@ public boolean getSuppressNarratives() {
 		return mySuppressNarratives;
 	}
 
-	protected boolean isChildContained(BaseRuntimeElementDefinition<?> childDef, boolean theIncludedResource) {
+	protected boolean isChildContained(
+			BaseRuntimeElementDefinition<?> childDef, boolean theIncludedResource, EncodeContext theContext) {
 		return (childDef.getChildType() == ChildTypeEnum.CONTAINED_RESOURCES
 						|| childDef.getChildType() == ChildTypeEnum.CONTAINED_RESOURCE_LIST)
-				&& getContainedResources().isEmpty() == false
+				&& theContext.getContainedResources().isEmpty() == false
 				&& theIncludedResource == false;
 	}
 
@@ -788,7 +789,8 @@ protected List<? extends IBase> preProcessValues(
 			 */
 			if (next instanceof IBaseReference) {
 				IBaseReference nextRef = (IBaseReference) next;
-				String refText = determineReferenceText(nextRef, theCompositeChildElement, theResource);
+				String refText =
+						determineReferenceText(nextRef, theCompositeChildElement, theResource, theEncodeContext);
 				if (!StringUtils.equals(refText, nextRef.getReferenceElement().getValue())) {
 
 					if (retVal == theValues) {
@@ -980,7 +982,7 @@ protected boolean shouldEncodeResource(String theName, EncodeContext theEncodeCo
 		return true;
 	}
 
-	protected void containResourcesInReferences(IBaseResource theResource) {
+	protected void containResourcesInReferences(IBaseResource theResource, EncodeContext theContext) {
 
 		/*
 		 * If a UUID is present in Bundle.entry.fullUrl but no value is present
@@ -1003,7 +1005,7 @@ protected void containResourcesInReferences(IBaseResource theResource) {
 			}
 		}
 
-		myContainedResources = getContext().newTerser().containResources(theResource);
+		theContext.setContainedResources(getContext().newTerser().containResources(theResource));
 	}
 
 	static class ChildNameAndDef {
@@ -1034,8 +1036,12 @@ class EncodeContext extends EncodeContextPath {
 		private final List<EncodeContextPath> myEncodeElementPaths;
 		private final Set<String> myEncodeElementsAppliesToResourceTypes;
 		private final List<EncodeContextPath> myDontEncodeElementPaths;
+		private FhirTerser.ContainedResources myContainedResources;
 
-		public EncodeContext(BaseParser theParser, ParserOptions theParserOptions) {
+		public EncodeContext(
+				BaseParser theParser,
+				ParserOptions theParserOptions,
+				FhirTerser.ContainedResources theContainedResources) {
 			Collection<String> encodeElements = theParser.myEncodeElements;
 			Collection<String> dontEncodeElements = theParser.myDontEncodeElements;
 			if (isSummaryMode()) {
@@ -1058,13 +1064,23 @@ public EncodeContext(BaseParser theParser, ParserOptions theParserOptions) {
 						dontEncodeElements.stream().map(EncodeContextPath::new).collect(Collectors.toList());
 			}
 
+			myContainedResources = theContainedResources;
+
 			myEncodeElementsAppliesToResourceTypes =
 					ParserUtil.determineApplicableResourceTypesForTerserPaths(myEncodeElementPaths);
 		}
 
 		private Map<Key, List<BaseParser.CompositeChildElement>> getCompositeChildrenCache() {
 			return myCompositeChildrenCache;
 		}
+
+		public FhirTerser.ContainedResources getContainedResources() {
+			return myContainedResources;
+		}
+
+		public void setContainedResources(FhirTerser.ContainedResources theContainedResources) {
+			myContainedResources = theContainedResources;
+		}
 	}
 
 	protected class CompositeChildElement {

diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java
@@ -54,6 +54,7 @@
 import ca.uhn.fhir.parser.json.jackson.JacksonStructure;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.util.ElementUtil;
+import ca.uhn.fhir.util.FhirTerser;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.text.WordUtils;
@@ -386,12 +387,14 @@ public String toString() {
 			}
 			case CONTAINED_RESOURCE_LIST:
 			case CONTAINED_RESOURCES: {
-				List<IBaseResource> containedResources = getContainedResources().getContainedResources();
+				List<IBaseResource> containedResources =
+						theEncodeContext.getContainedResources().getContainedResources();
 				if (containedResources.size() > 0) {
 					beginArray(theEventWriter, theChildName);
 
 					for (IBaseResource next : containedResources) {
-						IIdType resourceId = getContainedResources().getResourceId(next);
+						IIdType resourceId =
+								theEncodeContext.getContainedResources().getResourceId(next);
 						String value = resourceId.getValue();
 						encodeResourceToJsonStreamWriter(
 								theResDef,
@@ -554,7 +557,8 @@ private void encodeCompositeElementChildrenToStreamWriter(
 
 				if (nextValue == null || nextValue.isEmpty()) {
 					if (nextValue instanceof BaseContainedDt) {
-						if (theContainedResource || getContainedResources().isEmpty()) {
+						if (theContainedResource
+								|| theEncodeContext.getContainedResources().isEmpty()) {
 							continue;
 						}
 					} else {
@@ -838,7 +842,8 @@ public void encodeResourceToJsonLikeWriter(IBaseResource theResource, BaseJsonLi
 					+ theResource.getStructureFhirVersionEnum());
 		}
 
-		EncodeContext encodeContext = new EncodeContext(this, getContext().getParserOptions());
+		EncodeContext encodeContext =
+				new EncodeContext(this, getContext().getParserOptions(), new FhirTerser.ContainedResources());
 		String resourceName = getContext().getResourceType(theResource);
 		encodeContext.pushPath(resourceName, true);
 		doEncodeResourceToJsonLikeWriter(theResource, theJsonLikeWriter, encodeContext);
@@ -894,7 +899,7 @@ private void encodeResourceToJsonStreamWriter(
 		}
 
 		if (!theContainedResource) {
-			containResourcesInReferences(theResource);
+			containResourcesInReferences(theResource, theEncodeContext);
 		}
 
 		RuntimeResourceDefinition resDef = getContext().getResourceDefinition(theResource);

diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/RDFParser.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/RDFParser.java
@@ -191,7 +191,7 @@ private Resource encodeResourceToRDFStreamWriter(
 		}
 
 		if (!containedResource) {
-			containResourcesInReferences(resource);
+			containResourcesInReferences(resource, encodeContext);
 		}
 
 		if (!(resource instanceof IAnyResource)) {
@@ -354,7 +354,7 @@ private Model encodeChildElementToStreamWriter(
 		try {
 
 			if (element == null || element.isEmpty()) {
-				if (!isChildContained(childDef, includedResource)) {
+				if (!isChildContained(childDef, includedResource, theEncodeContext)) {
 					return rdfModel;
 				}
 			}

diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/XmlParser.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/XmlParser.java
@@ -295,7 +295,7 @@ private void encodeChildElementToStreamWriter(
 		try {
 
 			if (theElement == null || theElement.isEmpty()) {
-				if (isChildContained(childDef, theIncludedResource)) {
+				if (isChildContained(childDef, theIncludedResource, theEncodeContext)) {
 					// We still want to go in..
 				} else {
 					return;
@@ -359,8 +359,10 @@ private void encodeChildElementToStreamWriter(
 					 * theEventWriter.writeStartElement("contained"); encodeResourceToXmlStreamWriter(next, theEventWriter, true, fixContainedResourceId(next.getId().getValue()));
 					 * theEventWriter.writeEndElement(); }
 					 */
-					for (IBaseResource next : getContainedResources().getContainedResources()) {
-						IIdType resourceId = getContainedResources().getResourceId(next);
+					for (IBaseResource next :
+							theEncodeContext.getContainedResources().getContainedResources()) {
+						IIdType resourceId =
+								theEncodeContext.getContainedResources().getResourceId(next);
 						theEventWriter.writeStartElement("contained");
 						String value = resourceId.getValue();
 						encodeResourceToXmlStreamWriter(
@@ -682,7 +684,7 @@ private void encodeResourceToXmlStreamWriter(
 		}
 
 		if (!theContainedResource) {
-			containResourcesInReferences(theResource);
+			containResourcesInReferences(theResource, theEncodeContext);
 		}
 
 		theEventWriter.writeStartElement(resDef.getName());

diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/repository/Repository.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/repository/Repository.java
@@ -28,6 +28,8 @@
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException;
 import com.google.common.annotations.Beta;
+import com.google.common.collect.ArrayListMultimap;
+import com.google.common.collect.Multimap;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseConformance;
 import org.hl7.fhir.instance.model.api.IBaseParameters;
@@ -231,6 +233,23 @@ <T extends IBaseResource, I extends IIdType> MethodOutcome delete(
 
 	// Querying starts here
 
+	/**
+	 * Searches this repository
+	 *
+	 * @see <a href="https://www.hl7.org/fhir/http.html#search">FHIR search</a>
+	 *
+	 * @param <B> a Bundle type
+	 * @param <T> a Resource type
+	 * @param bundleType the class of the Bundle type to return
+	 * @param resourceType the class of the Resource type to search
+	 * @param searchParameters the searchParameters for this search
+	 * @return a Bundle with the results of the search
+	 */
+	default <B extends IBaseBundle, T extends IBaseResource> B search(
+			Class<B> bundleType, Class<T> resourceType, Multimap<String, List<IQueryParameterType>> searchParameters) {
+		return this.search(bundleType, resourceType, searchParameters, Collections.emptyMap());
+	}
+
 	/**
 	 * Searches this repository
 	 *
@@ -264,9 +283,32 @@ default <B extends IBaseBundle, T extends IBaseResource> B search(
 	<B extends IBaseBundle, T extends IBaseResource> B search(
 			Class<B> bundleType,
 			Class<T> resourceType,
-			Map<String, List<IQueryParameterType>> searchParameters,
+			Multimap<String, List<IQueryParameterType>> searchParameters,
 			Map<String, String> headers);
 
+	/**
+	 * Searches this repository
+	 *
+	 * @see <a href="https://www.hl7.org/fhir/http.html#search">FHIR search</a>
+	 *
+	 * @param <B> a Bundle type
+	 * @param <T> a Resource type
+	 * @param bundleType the class of the Bundle type to return
+	 * @param resourceType the class of the Resource type to search
+	 * @param searchParameters the searchParameters for this search
+	 * @param headers headers for this request, typically key-value pairs of HTTP headers
+	 * @return a Bundle with the results of the search
+	 */
+	default <B extends IBaseBundle, T extends IBaseResource> B search(
+			Class<B> bundleType,
+			Class<T> resourceType,
+			Map<String, List<IQueryParameterType>> searchParameters,
+			Map<String, String> headers) {
+		ArrayListMultimap<String, List<IQueryParameterType>> multimap = ArrayListMultimap.create();
+		searchParameters.forEach(multimap::put);
+		return this.search(bundleType, resourceType, multimap, headers);
+	}
+
 	// Paging starts here
 
 	/**