Merge remote-tracking branch 'origin/master'

README.md

@@ -43,7 +43,7 @@ correct implementation of the core FHIR specification that it implements.
 
 ### Prerequisites
 
-This project uses [Java](https://www.java.com) (minumum version 11), [Apache Maven](http://maven.apache.org), and [Lombok](https://projectlombok.org/) to build. You can find detailed instructions on setting up this project in your IDE [here](https://hl7.github.io/docs/core/ide).
+This project uses [Java](https://www.java.com) (minumum version 11), [Apache Maven](http://maven.apache.org), and [Lombok](https://projectlombok.org/) to build. You can find detailed instructions on setting up this project in your IDE [here](https://hl7.github.io/docs/core/getting-started).
 
 ### Build Commands
 

RELEASE_NOTES.md

@@ -1,7 +1,12 @@
 ## Validator Changes
 
-* no changes
+* Fix for NPE rendering resources
 
 ## Other code changes
 
-* no changes
+* XHTML processing: Cater for "." in XML element and attribute names
+* Handle R3 encoding of primitive values when validating profiles
+* Improve error messaging when validating StructureDefinition
+* Temporary Support for MedicationStatement in R5
+* Rework Package API to allow for authentication on package servers
+* Structure mapping now finds source Structure Definition by URI and sets ParserBase logical property appropriately.

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/context/IWorkerContext.java

@@ -299,6 +299,8 @@ public interface IWorkerContext {
 
   String formatMessage(String theMessage, Object... theMessageArguments);
 
+  String formatMessagePlural(Integer pl, String theMessage, Object... theMessageArguments);
+
   void setValidationMessageLanguage(Locale locale);
 
   public class ValidationResult {

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/FHIRPathEngine.java

@@ -575,7 +575,7 @@ public class FHIRPathEngine {
   }
 
   private FHIRException makeExceptionPlural(Integer num, ExpressionNode holder, String constName, Object... args) {
-    String fmt = worker.formatMessage(constName, args);
+    String fmt = worker.formatMessagePlural(num, constName, args);
     if (location != null) {
       fmt = fmt + " "+worker.formatMessage(I18nConstants.FHIRPATH_LOCATION, location);
     }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/structuremap/FFHIRPathHostServices.java

@@ -96,7 +96,7 @@ public class FFHIRPathHostServices implements FHIRPathEngine.IEvaluationContext
 
   @Override
   public ValueSet resolveValueSet(Object appContext, String url) {
-    throw new Error("Not Implemented Yet");
+	return structureMapUtilities.getWorker().fetchResource(ValueSet.class, url);
   }
 
 }

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/utils/structuremap/FFHIRPathHostServicesTest.java

@@ -0,0 +1,31 @@
+package org.hl7.fhir.r5.utils.structuremap;
+
+import java.io.IOException;
+
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.r5.context.SimpleWorkerContext;
+import org.hl7.fhir.r5.model.ValueSet;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
+import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+
+class FFHIRPathHostServicesTest {
+  static private SimpleWorkerContext context;
+
+  @BeforeAll
+  static public void setUp() throws Exception {
+    FilesystemPackageCacheManager pcm = new org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager(false);
+    context = TestingUtilities.getWorkerContext(pcm.loadPackage("hl7.fhir.r4.core", "4.0.1"));
+  }
+
+  @Test
+  public void testrResolveValueSet() throws IOException, FHIRException {
+    StructureMapUtilities scu = new StructureMapUtilities(context);
+    FFHIRPathHostServices fphs = new FFHIRPathHostServices(scu);
+    ValueSet v = fphs.resolveValueSet(null, "http://hl7.org/fhir/ValueSet/FHIR-version");
+    Assertions.assertNotNull(v);
+    Assertions.assertEquals("http://hl7.org/fhir/ValueSet/FHIR-version", v.getUrl());
+  }
+}

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java

@@ -36,6 +36,7 @@ import org.hl7.fhir.r5.elementmodel.Element;
 import org.hl7.fhir.r5.elementmodel.Manager;
 import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
 import org.hl7.fhir.r5.elementmodel.ObjectConverter;
+import org.hl7.fhir.r5.elementmodel.ParserBase;
 import org.hl7.fhir.r5.elementmodel.SHCParser;
 import org.hl7.fhir.r5.formats.FormatUtilities;
 import org.hl7.fhir.r5.formats.IParser.OutputStyle;
@@ -623,10 +624,15 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
   public org.hl7.fhir.r5.elementmodel.Element transform(byte[] source, FhirFormat cntType, String mapUri) throws FHIRException, IOException {
     List<Base> outputs = new ArrayList<>();
     StructureMapUtilities scu = new StructureMapUtilities(context, new TransformSupportServices(outputs, mapLog, context));
-    org.hl7.fhir.r5.elementmodel.Element src = Manager.parseSingle(context, new ByteArrayInputStream(source), cntType);
     StructureMap map = context.fetchResource(StructureMap.class, mapUri);
     if (map == null) throw new Error("Unable to find map " + mapUri + " (Known Maps = " + context.listMapUrls() + ")");
     org.hl7.fhir.r5.elementmodel.Element resource = getTargetResourceFromStructureMap(map);
+    StructureDefinition sourceSD = getSourceResourceFromStructureMap(map);
+    ParserBase parser = Manager.makeParser(context, cntType);
+    if (sourceSD.getKind() == StructureDefinition.StructureDefinitionKind.LOGICAL) {
+      parser.setLogical(sourceSD);
+    }
+    org.hl7.fhir.r5.elementmodel.Element src = parser.parseSingle(new ByteArrayInputStream(source));    
     scu.transform(null, src, map, resource);
     resource.populatePaths(null);
     return resource;
@@ -655,6 +661,39 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
 
     return Manager.build(getContext(), structureDefinition);
   }
+  
+  private StructureDefinition getSourceResourceFromStructureMap(StructureMap map) {
+	StructureMap.StructureMapGroupComponent g = map.getGroup().get(0);
+	String type = null;
+	for (StructureMap.StructureMapGroupInputComponent inp : g.getInput()) {
+	  if (inp.getMode() == StructureMap.StructureMapInputMode.SOURCE)
+	    if (type != null)
+	      throw new DefinitionException("This engine does not support multiple source inputs");
+	    else
+	      type = inp.getType();
+	}	  
+	  
+	String sourceTypeUrl = null;
+	for (StructureMap.StructureMapStructureComponent component : map.getStructure()) {
+	  if (component.getMode() == StructureMap.StructureMapModelMode.SOURCE
+	      && component.getAlias().equalsIgnoreCase(type)) {
+	    sourceTypeUrl = component.getUrl();
+	    break;
+	  }
+	}
+	    
+	StructureDefinition structureDefinition = null;
+	for (StructureDefinition sd : this.context.fetchResourcesByType(StructureDefinition.class)) {
+	  if (sd.getUrl().equalsIgnoreCase(sourceTypeUrl)) {
+	    structureDefinition = sd;
+	  	break;
+	  }
+	}
+
+	if (structureDefinition == null) throw new FHIRException("Unable to find StructureDefinition for source type ('" + sourceTypeUrl + "')");
+	return structureDefinition;
+  }
+
 
   public Resource generate(String source, String version) throws FHIRException, IOException, EOperationOutcome {
     Content cnt = igLoader.loadContent(source, "validate", false);

org.hl7.fhir.validation/src/test/java/org/hl7/fhir/r5/test/StructureMappingTests.java

@@ -1,6 +1,7 @@
 package org.hl7.fhir.r5.test;
 
 import static org.junit.Assert.assertTrue;
+import static org.junit.jupiter.api.Assertions.assertThrows;
 import static org.junit.jupiter.api.Assertions.fail;
 
 import java.io.*;
@@ -10,6 +11,7 @@ import java.util.stream.Stream;
 
 import javax.xml.parsers.ParserConfigurationException;
 
+import org.hl7.fhir.exceptions.DefinitionException;
 import org.hl7.fhir.r5.context.ContextUtilities;
 import org.hl7.fhir.r5.context.SimpleWorkerContext;
 import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
@@ -25,7 +27,9 @@ import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.hl7.fhir.validation.ValidationEngine;
 import org.hl7.fhir.validation.instance.InstanceValidatorFactory;
+import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.Arguments;
 import org.junit.jupiter.params.provider.MethodSource;
@@ -123,4 +127,48 @@ public class StructureMappingTests {
     }
     assertTrue(msg, Utilities.noString(msg));
   }
+  @Test
+  void testTransformLogicalSource() throws Exception {
+    String map = "map \"http://github.com/hapifhir/org.hl7.fhir.core/org.hl7.fhir.r4.tests/cda2qr\" = \"cda2qr\"\n"
+    		+ "\n"
+    		+ "uses \"http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse\" alias QuestionnaireResponse as target\n"
+    		+ "uses \"http://hl7.org/fhir/cdatest/StructureDefinition/ClinicalDocument\" alias ClinicalDocument as source\n"
+    		+ "\n"
+    		+ "group ClinicalDocument(source src : ClinicalDocument, target tgt : QuestionnaireResponse) {\n"
+    		+ "  src -> tgt.status = 'in-progress' \"code\";\n"
+    		+ "}";
+    StructureMap r = null;   
+	try {
+	  r = new StructureMapUtilities(context).parse(map, "cda2qr");
+	  context.cacheResource(r);	      
+	  byte[] byteSource = "{}".getBytes();
+	  org.hl7.fhir.r5.elementmodel.Element element = validationEngine.transform(byteSource, FhirFormat.JSON, r.getUrl());
+	  Assertions.assertNotNull(element);
+	} finally {
+	  context.dropResource(r);
+	}      
+  }  
+  @Test
+  void testGetSourceResourceFromStructureMapDefinitionException() {
+    StructureMap r = new StructureMap().setUrl("testGetSourceResourceFromStructureMapDefinitionException");      
+    StructureMap.StructureMapGroupComponent g = r.addGroup();
+    g.addInput().setMode(StructureMap.StructureMapInputMode.SOURCE).setType("input");
+    g.addInput().setMode(StructureMap.StructureMapInputMode.SOURCE).setType("input");
+    r.addStructure()
+      .setMode(StructureMap.StructureMapModelMode.TARGET)
+      .setUrl("testGetSourceResourceFromStructureMapDefinitionExceptionTarget");
+    context.cacheResource(r);
+    StructureDefinition structureDefinition = new StructureDefinition().setUrl("testGetSourceResourceFromStructureMapDefinitionExceptionTarget");
+    structureDefinition.getSnapshot().addElement().setPath("testGetSourceResourceFromStructureMapDefinitionExceptionTarget");
+    context.cacheResource(structureDefinition);
+    byte[] byteSource = "testGetSourceResourceFromStructureMapDefinitionException".getBytes();
+    DefinitionException thrown = assertThrows(
+    		DefinitionException.class,
+    		() -> validationEngine.transform(byteSource, FhirFormat.JSON, r.getUrl()),
+    		"Expected transform() to throw DefinitionException"
+    		);
+    context.dropResource(r);
+    context.dropResource(structureDefinition);
+    assertTrue(thrown.getMessage().contentEquals("This engine does not support multiple source inputs"));
+  }
 }