Merge branch 'hapifhir:master' into update_packages

Author: madduci

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

@@ -1475,33 +1475,27 @@ public boolean acceptUndeclaredExtension(
 	}
 
 	/**
-	 * Clear all content on a resource
+	 * Clear all content on an element
+	 *
+	 * @return Returns <code>true</code> if any content was actually cleared
+	 * @since 8.6.0
 	 */
-	public void clear(IBaseResource theInput) {
-		visit(theInput, new IModelVisitor2() {
-			@Override
-			public boolean acceptElement(
-					IBase theElement,
-					List<IBase> theContainingElementPath,
-					List<BaseRuntimeChildDefinition> theChildDefinitionPath,
-					List<BaseRuntimeElementDefinition<?>> theElementDefinitionPath) {
-				if (theElement instanceof IPrimitiveType) {
-					((IPrimitiveType) theElement).setValueAsString(null);
-				}
-				return true;
-			}
+	public boolean clear(IBase theInput) {
+		ClearingModelVisitor visitor = new ClearingModelVisitor();
+		visit(theInput, visitor);
+		return visitor.myFoundContent;
+	}
 
-			@Override
-			public boolean acceptUndeclaredExtension(
-					IBaseExtension<?, ?> theNextExt,
-					List<IBase> theContainingElementPath,
-					List<BaseRuntimeChildDefinition> theChildDefinitionPath,
-					List<BaseRuntimeElementDefinition<?>> theElementDefinitionPath) {
-				theNextExt.setUrl(null);
-				theNextExt.setValue(null);
-				return true;
-			}
-		});
+	/**
+	 * Clear all content on a resource.
+	 *
+	 * @return Returns <code>true</code> if any content was actually cleared
+	 * @see #clear(IBase) This method is a synonym for {@link #clear(IBase)}, provided for historical reasons.
+	 */
+	public boolean clear(IBaseResource theInput) {
+		ClearingModelVisitor visitor = new ClearingModelVisitor();
+		visit(theInput, visitor);
+		return visitor.myFoundContent;
 	}
 
 	private void containResourcesForEncoding(ContainedResources theContained, IBaseResource theResource) {
@@ -2003,4 +1997,45 @@ public IIdType getPreviouslyContainedResourceId(IBaseResource theResource) {
 			return null;
 		}
 	}
+
+	private static class ClearingModelVisitor implements IModelVisitor2 {
+
+		private boolean myFoundContent;
+
+		@Override
+		public boolean acceptElement(
+				IBase theElement,
+				List<IBase> theContainingElementPath,
+				List<BaseRuntimeChildDefinition> theChildDefinitionPath,
+				List<BaseRuntimeElementDefinition<?>> theElementDefinitionPath) {
+			if (theElement instanceof IPrimitiveType<?> type) {
+				if (type.getValueAsString() != null) {
+					myFoundContent = true;
+					type.setValueAsString(null);
+				}
+			}
+			return true;
+		}
+
+		@Override
+		public boolean acceptUndeclaredExtension(
+				IBaseExtension<?, ?> theNextExt,
+				List<IBase> theContainingElementPath,
+				List<BaseRuntimeChildDefinition> theChildDefinitionPath,
+				List<BaseRuntimeElementDefinition<?>> theElementDefinitionPath) {
+			if (theNextExt.getUrl() != null) {
+				theNextExt.setUrl(null);
+				myFoundContent = true;
+			}
+			if (theNextExt.getValue() != null) {
+				myFoundContent = true;
+				theNextExt.setValue(null);
+			}
+			if (!theNextExt.getExtension().isEmpty()) {
+				theNextExt.getExtension().clear();
+				myFoundContent = true;
+			}
+			return true;
+		}
+	}
 }

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

@@ -234,6 +234,19 @@ public static Optional<Integer> getParameterPartValueAsInteger(
 				.map(t -> (Integer) t);
 	}
 
+	/**
+	 * @since 8.6.0
+	 */
+	public static Optional<Boolean> getParameterPartValueAsBoolean(
+			FhirContext theCtx, IBase theParameter, String theParameterName) {
+		return getParameterPartValue(theCtx, theParameter, theParameterName)
+				.filter(t -> IPrimitiveType.class.isAssignableFrom(t.getClass()))
+				.map(t -> (IPrimitiveType<?>) t)
+				.map(IPrimitiveType::getValue)
+				.filter(t -> Boolean.class.isAssignableFrom(t.getClass()))
+				.map(t -> (Boolean) t);
+	}
+
 	private static <T> List<T> extractNamedParameterValues(
 			FhirContext theCtx,
 			IBaseParameters theParameters,
@@ -481,8 +494,11 @@ public static void addPartUrl(FhirContext theContext, IBase theParameter, String
 		addPart(theContext, theParameter, theName, value);
 	}
 
-	public static void addPartBoolean(FhirContext theContext, IBase theParameter, String theName, Boolean theValue) {
-		addPart(theContext, theParameter, theName, theContext.newPrimitiveBoolean(theValue));
+	/**
+	 * @return Returns the added part
+	 */
+	public static IBase addPartBoolean(FhirContext theContext, IBase theParameter, String theName, Boolean theValue) {
+		return addPart(theContext, theParameter, theName, theContext.newPrimitiveBoolean(theValue));
 	}
 
 	public static void addPartDecimal(FhirContext theContext, IBase theParameter, String theName, Double theValue) {

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

@@ -33,12 +33,12 @@
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
-import java.io.UnsupportedEncodingException;
 import java.net.MalformedURLException;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.net.URL;
 import java.net.URLDecoder;
+import java.nio.charset.StandardCharsets;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.ArrayList;
@@ -559,13 +559,7 @@ public static String unescape(String theString) {
 		for (int i = 0; i < theString.length(); i++) {
 			char nextChar = theString.charAt(i);
 			if (nextChar == '%' || (nextChar == '+' && shouldEscapePlus)) {
-				try {
-					// Yes it would be nice to not use a string "UTF-8" but the equivalent
-					// method that takes Charset is JDK10+ only... sigh....
-					return URLDecoder.decode(theString, "UTF-8");
-				} catch (UnsupportedEncodingException e) {
-					throw new Error(Msg.code(1743) + "UTF-8 not supported, this shouldn't happen", e);
-				}
+				return URLDecoder.decode(theString, StandardCharsets.UTF_8);
 			}
 		}
 		return theString;

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

@@ -132,8 +132,6 @@ public VersionCanonicalizer(FhirContext theTargetContext) {
 		}
 	}
 
-	@SuppressWarnings({"EnhancedSwitchMigration"})
-
 	/**
 	 * Canonical version: R5
 	 */
@@ -315,6 +313,10 @@ public SubscriptionTopic subscriptionTopicToCanonical(IBaseResource theResource)
 		return SubscriptionTopicCanonicalizer.canonicalizeTopic(myContext, theResource);
 	}
 
+	public IBaseResource conceptMapFromCanonical(ConceptMap theConceptMap) {
+		return myStrategy.conceptMapFromCanonical(theConceptMap);
+	}
+
 	private interface IStrategy {
 
 		CapabilityStatement capabilityStatementToCanonical(IBaseResource theCapabilityStatement);
@@ -333,6 +335,8 @@ private interface IStrategy {
 
 		ConceptMap conceptMapToCanonical(IBaseResource theConceptMap);
 
+		IBaseResource conceptMapFromCanonical(ConceptMap theConceptMap);
+
 		SearchParameter searchParameterToCanonical(IBaseResource theSearchParameter);
 
 		IBaseParameters parametersFromCanonical(Parameters theParameters);
@@ -465,6 +469,13 @@ public ConceptMap conceptMapToCanonical(IBaseResource theConceptMap) {
 			return (ConceptMap) VersionConvertorFactory_10_40.convertResource(reencoded, ADVISOR_10_40);
 		}
 
+		@Override
+		public IBaseResource conceptMapFromCanonical(ConceptMap theConceptMap) {
+			Resource codeSystemDstu2Hl7Org =
+					VersionConvertorFactory_10_40.convertResource(theConceptMap, ADVISOR_10_40);
+			return reencodeFromHl7Org(codeSystemDstu2Hl7Org);
+		}
+
 		@Override
 		public SearchParameter searchParameterToCanonical(IBaseResource theSearchParameter) {
 			org.hl7.fhir.dstu2.model.SearchParameter reencoded =
@@ -620,6 +631,11 @@ public ConceptMap conceptMapToCanonical(IBaseResource theConceptMap) {
 					(org.hl7.fhir.dstu2016may.model.Resource) theConceptMap, ADVISOR_14_40);
 		}
 
+		@Override
+		public IBaseResource conceptMapFromCanonical(ConceptMap theConceptMap) {
+			return VersionConvertorFactory_14_40.convertResource(theConceptMap, ADVISOR_14_40);
+		}
+
 		@Override
 		public SearchParameter searchParameterToCanonical(IBaseResource theSearchParameter) {
 			return (SearchParameter) VersionConvertorFactory_14_50.convertResource(
@@ -729,6 +745,11 @@ public ConceptMap conceptMapToCanonical(IBaseResource theConceptMap) {
 					(org.hl7.fhir.dstu3.model.Resource) theConceptMap, ADVISOR_30_40);
 		}
 
+		@Override
+		public IBaseResource conceptMapFromCanonical(ConceptMap theConceptMap) {
+			return VersionConvertorFactory_30_40.convertResource(theConceptMap, ADVISOR_30_40);
+		}
+
 		@Override
 		public SearchParameter searchParameterToCanonical(IBaseResource theSearchParameter) {
 			return (SearchParameter) VersionConvertorFactory_30_50.convertResource(
@@ -832,6 +853,11 @@ public ConceptMap conceptMapToCanonical(IBaseResource theConceptMap) {
 			return (ConceptMap) theConceptMap;
 		}
 
+		@Override
+		public IBaseResource conceptMapFromCanonical(ConceptMap theConceptMap) {
+			return theConceptMap;
+		}
+
 		@Override
 		public SearchParameter searchParameterToCanonical(IBaseResource theSearchParameter) {
 			return (SearchParameter) VersionConvertorFactory_40_50.convertResource(
@@ -957,6 +983,13 @@ public ConceptMap conceptMapToCanonical(IBaseResource theConceptMap) {
 			return (ConceptMap) VersionConvertorFactory_40_50.convertResource(conceptMapR5, ADVISOR_40_50);
 		}
 
+		@Override
+		public IBaseResource conceptMapFromCanonical(ConceptMap theConceptMap) {
+			org.hl7.fhir.r5.model.ConceptMap conceptMapR5 = (org.hl7.fhir.r5.model.ConceptMap)
+					VersionConvertorFactory_40_50.convertResource(theConceptMap, ADVISOR_40_50);
+			return VersionConvertorFactory_43_50.convertResource(conceptMapR5, ADVISOR_43_50);
+		}
+
 		@Override
 		public SearchParameter searchParameterToCanonical(IBaseResource theSearchParameter) {
 			return (SearchParameter) VersionConvertorFactory_43_50.convertResource(
@@ -1069,6 +1102,11 @@ public ConceptMap conceptMapToCanonical(IBaseResource theConceptMap) {
 					(org.hl7.fhir.r5.model.ConceptMap) theConceptMap, ADVISOR_40_50);
 		}
 
+		@Override
+		public IBaseResource conceptMapFromCanonical(ConceptMap theConceptMap) {
+			return VersionConvertorFactory_40_50.convertResource(theConceptMap, ADVISOR_40_50);
+		}
+
 		@Override
 		public SearchParameter searchParameterToCanonical(IBaseResource theSearchParameter) {
 			return (SearchParameter) theSearchParameter;

hapi-fhir-converter/src/main/java/ca/uhn/hapi/converters/canonical/VersionCanonicalizer.java

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 7210
+jira: SMILE-9866
+title: "Previously, bulk exports were not using the resource whitelist nor the search parameter 
+    enable/disable patterns. This has been fixed."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/8_6_0/7210-use-resource-whitelist-during-bulk-export.yaml

@@ -0,0 +1,6 @@
+---
+type: add
+issue: 7275
+title: "A new utility class called FhirPatchBuilder has been added. This class can be used to
+   programmatically generate FHIR Patch documents. See [FHIR Patch](https://smilecdr.com/docs/fhir_standard/fhir_patch.html) for
+   examples on how to use this class."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/8_6_0/7275-add-fhir-patch-builder.yaml

@@ -0,0 +1,16 @@
+---
+type: fix
+issue: 7275
+title: "A number of new test cases and fixes have been added to the HAPI FHIR FHIRPath Patch engine:
+  <ul>
+    <li>
+      Replace and Delete operations containing FHIRPath expressions where the final element was
+      a filter (such as <code>Observation.code.coding.where(system='http://loinc.org')</code>)
+      would fail if the system URL contained a dot character.
+    </li>
+    <li>
+      Insert operations can now add an extension to an anonymous element, as shown in the
+      FHIR specification
+      <a href=\"https://hl7.org/fhir/fhirpatch.html#extension\">Extension Example</a>.
+    </li>
+  </ul>"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/8_6_0/7275-fhir-patch-fixes.yaml

@@ -0,0 +1,7 @@
+---
+type: add
+issue: 7275
+title: "A HAPI FHIR extension to the FHIR Patch specification has been added, which permits the
+   **delete** operation to find and delete multiple elements matching a single FHIRPath expression.
+   See [Deleting Multiple Elements](https://smilecdr.com/docs/fhir_standard/fhir_patch.html#multi-delete) for
+   examples on how to use this feature."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/8_6_0/7275-fhir-patch-multi-delete.yaml

@@ -0,0 +1,6 @@
+---
+type: add
+issue: 7276
+title: "Two new operations have been added to the JPA server called `ConceptMap/$hapi.fhir.add-mapping`
+   and `ConceptMap/$hapi.fhir.remove-mapping`. These operations can be used to add or remove individual
+   entries within a ConceptMap resource."