Merge pull request #1569 from hapifhir/2024-02-gg-pat-cont-resources

2024 02 gg pat cont resources

RELEASE_NOTES.md

@@ -18,6 +18,7 @@
 * Fix where validator was ignoring minimum cardinality for XML attributes (especially in CDA)
 * Improved ConceptMap validation
 * Updated IG versions used for -cda and -ccda CLI validation options.
+* Change validator so that it marks value properties in primitive data types as illegal
 
 ## Other code changes
 
@@ -32,3 +33,8 @@
 * Fix wrong URLs rendering Profiles and Questionnaires
 * Fix bug using wrong version constant for R3
 * Updates for R5 StructureMap syntax
+* Support for case sensitive Code system tests
+* Add TurtleGeneratorTests for R5
+* Introduce new validator cliContext option disableDefaultResourceFetcher (#1526)
+* Render contained resources when rendering Patient resources 
+* Fix bug in FML Parser 

org.hl7.fhir.convertors/src/test/java/org/hl7/fhir/convertors/Convertor_Factory_40_50Test.java

@@ -66,14 +66,14 @@ class Convertor_Factory_40_50Test  {
     StructureMapUtilities smu5 = new StructureMapUtilities(context, mock(org.hl7.fhir.r5.utils.structuremap.ITransformerServices.class));
     org.hl7.fhir.r5.model.StructureMap mapR5 = smu5.parse(CONTENT, "map");
 
-    assertEquals("tgt", mapR5.getGroup().get(0).getRule().get(0).getTarget().get(0).getParameter().get(0).getValueIdType().getValue());
+    assertEquals("tgt", mapR5.getGroup().get(0).getRule().get(0).getTarget().get(0).getContext());
     assertEquals("item.answer.valueString", mapR5.getGroup().get(1).getRule().get(0).getTarget().get(0).getParameter().get(0).getValueStringType().getValue());
     assertEquals("item", mapR5.getGroup().get(0).getRule().get(0).getDependent().get(0).getParameter().get(0).getValueIdType().getValueAsString());
     assertEquals("patient", mapR5.getGroup().get(0).getRule().get(0).getDependent().get(0).getParameter().get(1).getValueIdType().getValueAsString());
 
 
     org.hl7.fhir.r4.model.StructureMap mapR4 = (org.hl7.fhir.r4.model.StructureMap) VersionConvertorFactory_40_50.convertResource(mapR5);
-    assertEquals("tgt", mapR4.getGroup().get(0).getRule().get(0).getTarget().get(0).getParameter().get(0).getValueIdType().getValue());
+    assertEquals("tgt", mapR4.getGroup().get(0).getRule().get(0).getTarget().get(0).getContext());
     assertEquals("item.answer.valueString", mapR4.getGroup().get(1).getRule().get(0).getTarget().get(0).getParameter().get(0).getValueStringType().getValue());
     assertEquals("item", mapR4.getGroup().get(0).getRule().get(0).getDependent().get(0).getVariable().get(0).getValueAsString());
     assertEquals("patient", mapR4.getGroup().get(0).getRule().get(0).getDependent().get(0).getVariable().get(1).getValueAsString());
@@ -87,7 +87,7 @@ class Convertor_Factory_40_50Test  {
 
 
     StructureMap mapR5Back = (StructureMap) VersionConvertorFactory_40_50.convertResource(mapR4);
-    assertEquals("tgt", mapR5Back.getGroup().get(0).getRule().get(0).getTarget().get(0).getParameter().get(0).getValueIdType().getValue());
+    assertEquals("tgt", mapR5Back.getGroup().get(0).getRule().get(0).getTarget().get(0).getContext());
     assertEquals("item.answer.valueString", mapR5Back.getGroup().get(1).getRule().get(0).getTarget().get(0).getParameter().get(0).getValueStringType().getValue());
     assertEquals("item", mapR5Back.getGroup().get(0).getRule().get(0).getDependent().get(0).getParameter().get(0).getValueIdType().getValueAsString());
     assertEquals("patient", mapR5Back.getGroup().get(0).getRule().get(0).getDependent().get(0).getParameter().get(1).getValueIdType().getValueAsString());

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/PatientRenderer.java

@@ -32,6 +32,7 @@ import org.hl7.fhir.r5.renderers.utils.BaseWrappers.BaseWrapper;
 import org.hl7.fhir.r5.renderers.utils.BaseWrappers.PropertyWrapper;
 import org.hl7.fhir.r5.renderers.utils.BaseWrappers.ResourceWrapper;
 import org.hl7.fhir.r5.renderers.utils.RenderingContext;
+import org.hl7.fhir.r5.utils.EOperationOutcome;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
@@ -269,7 +270,7 @@ public class PatientRenderer extends ResourceRenderer {
   }
 
   @Override
-  public boolean render(XhtmlNode x, ResourceWrapper r) throws FHIRFormatError, DefinitionException, IOException {
+  public boolean render(XhtmlNode x, ResourceWrapper r) throws IOException, FHIRException, EOperationOutcome {
     // banner
     describe(makeBanner(x.para()), r);
     x.hr();
@@ -295,9 +296,22 @@ public class PatientRenderer extends ResourceRenderer {
     if (tbl.isEmpty()) {
       x.remove(tbl);
     }
+    if (r.has("contained") && context.isTechnicalMode()) {
+      x.hr();
+      x.para().b().tx("Contained Resources");
+      addContained(x, r.getContained());
+    }
     return false;
   }
 
+  private void addContained(XhtmlNode x, List<ResourceWrapper> list) throws FHIRFormatError, DefinitionException, FHIRException, IOException, EOperationOutcome {
+    for (ResourceWrapper c : list) {
+      x.hr();
+      x.an(c.getId());
+      new RendererFactory().factory(c, context).render(x, c);
+    }
+  }
+
   private void addExtensions(XhtmlNode tbl, ResourceWrapper r) throws UnsupportedEncodingException, FHIRException, IOException {
     Map<String, List<Extension>> extensions = new HashMap<>();
     PropertyWrapper pw = getProperty(r, "extension");

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

@@ -1141,6 +1141,7 @@ public class StructureMapUtilities {
       }
       lexer.token(")");
     } else if (name != null) {
+      if (target.getContext() != null) {
         target.setTransform(StructureMapTransform.COPY);
         if (!isConstant) {
           String id = name;
@@ -1150,6 +1151,9 @@ public class StructureMapUtilities {
           target.addParameter().setValue(new IdType(id));
         } else
           target.addParameter().setValue(readConstant(name, lexer));
+      } else {
+        target.setContext(name);
+      }
     }
     if (lexer.hasToken("as")) {
       lexer.take();
@@ -1716,10 +1720,9 @@ public class StructureMapUtilities {
     Base dest = null;
     if (tgt.hasContext()) {
       dest = vars.get(VariableMode.OUTPUT, tgt.getContext());
-      if (dest == null)
+      if (dest == null) {
-        throw new FHIRException("Rule \"" + rulePath + "\": target context not known: " + tgt.getContext());
+        throw new FHIRException("Rul \"" + rulePath + "\": target context not known: " + tgt.getContext());
-      if (!tgt.hasElement())
+      }
-        throw new FHIRException("Rule \"" + rulePath + "\": Not supported yet");
     }
     Base v = null;
     if (tgt.hasTransform()) {
@@ -1738,8 +1741,10 @@ public class StructureMapUtilities {
           v = dest.makeProperty(tgt.getElement().hashCode(), tgt.getElement());
           sharedVars.add(VariableMode.SHARED, tgt.getListRuleId(), v);
         }
-      } else {
+      } else if (tgt.hasElement()) {
         v = dest.makeProperty(tgt.getElement().hashCode(), tgt.getElement());
+      } else {
+        v = dest;
       }
     }
     if (tgt.hasVariable() && v != null)

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/VersionUtilities.java

@@ -703,7 +703,11 @@ public class VersionUtilities {
   }
 
   public static String getNameForVersion(String v) {
-    switch (getMajMin(v)) {
+    String mm = getMajMin(v);
+    if (mm == null) {
+      throw new Error("Unable to determine version for '"+v+"'");
+    }
+    switch (mm) {
     case "1.0" : return "R2";
     case "1.4" : return "R2B";
     case "3.0" : return "R3";

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java

@@ -1059,6 +1059,7 @@ public class I18nConstants {
   public static final String VALUESET_INCLUDE_CSVER_MULTI_FOUND = "VALUESET_INCLUDE_CSVER_MULTI_FOUND";
   public static final String UNABLE_TO_INFER_CODESYSTEM = "UNABLE_TO_INFER_CODESYSTEM";
   public static final String CODE_CASE_DIFFERENCE = "CODE_CASE_DIFFERENCE";
+  public static final String ILLEGAL_PROPERTY = "ILLEGAL_PROPERTY";
 }
 
 

org.hl7.fhir.utilities/src/main/resources/Messages.properties

@@ -1117,3 +1117,4 @@ VALUESET_INCLUDE_CS_MULTI_FOUND = Multiple matching contained code systems found
 VALUESET_INCLUDE_CSVER_MULTI_FOUND = Multiple matching contained code systems found for system ''{0}'' version ''{1}''
 CODE_CASE_DIFFERENCE = The code ''{0}'' differs from the correct code ''{1}'' by case. Although the code system ''{2}'' is case insensitive, implementers are strongly encouraged to use the correct case anyway
 SCT_NO_MRCM = Not validated against the Machine Readable Concept Model (MRCM)
+ILLEGAL_PROPERTY = The property ''{0}'' is invalid

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java

@@ -2627,6 +2627,12 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
 
   private boolean checkPrimitive(ValidationContext valContext, List<ValidationMessage> errors, String path, String type, ElementDefinition context, Element e, StructureDefinition profile, NodeStack node, NodeStack parentNode, Element resource) throws FHIRException {
     boolean ok = true;
+
+    // sanity check. The only children allowed are id and extension, but value might slip through in some circumstances. 
+    for (Element child : e.getChildren()) {
+      ok = rule(errors, "2024-02-28", IssueType.INVALID, child.line(), child.col(), path, !"value".equals(child.getName()), I18nConstants.ILLEGAL_PROPERTY, "value") && ok;
+    }
+    
     if (isBlank(e.primitiveValue())) {
       if (e.primitiveValue() == null)
         ok = rule(errors, NO_RULE_DATE, IssueType.INVALID, e.line(), e.col(), path, e.hasChildren(), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_PRIMITIVE_VALUEEXT) && ok;
@@ -6116,7 +6122,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
       }
       childDefinitions = getActualTypeChildren(valContext, element, actualType);
     } else if (definition.getType().size() > 1) {
-      // this only happens when the profile constrains the abstract children but leaves th choice open.
+      // this only happens when the profile constrains the abstract children but leaves the choice open.
       if (actualType == null) {
         vi.setValid(false);
         return false; // there'll be an error elsewhere in this case, and we're going to stop.

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

@@ -1,4 +1,4 @@
-package org.hl7.fhir.r5.test;
+package org.hl7.fhir.validation.tests;
 
 import static org.junit.Assert.assertTrue;
 import static org.junit.jupiter.api.Assertions.assertThrows;

pom.xml

@@ -20,7 +20,7 @@
     <properties>
         <guava_version>32.0.1-jre</guava_version>
         <hapi_fhir_version>6.4.1</hapi_fhir_version>
-        <validator_test_case_version>1.4.29-SNAPSHOT</validator_test_case_version>
+        <validator_test_case_version>1.5.0-SNAPSHOT</validator_test_case_version>
         <jackson_version>2.16.0</jackson_version>
         <junit_jupiter_version>5.9.2</junit_jupiter_version>
         <junit_platform_launcher_version>1.8.2</junit_platform_launcher_version>