Merge pull request #1447 from hapifhir/2023-09-gg-cda-fixes

2023 09 gg cda fixes

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/profile/ProfileUtilities.java

@@ -92,6 +92,7 @@ import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionMappingCompo
 import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionSnapshotComponent;
 import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
 import org.hl7.fhir.r5.model.UriType;
+import org.hl7.fhir.r5.model.UsageContext;
 import org.hl7.fhir.r5.model.ValueSet;
 import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionComponent;
 import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
@@ -2691,6 +2692,14 @@ public class ProfileUtilities extends TranslatingUtilities {
           if (d.hasValueSet()) {
             nb.setValueSet(d.getValueSet());
           }
+          for (ElementDefinitionBindingAdditionalComponent ab : d.getAdditional()) {
+            ElementDefinitionBindingAdditionalComponent eab = getMatchingAdditionalBinding(nb, ab);
+            if (eab != null) {
+              mergeAdditionalBinding(eab, ab);
+            } else {
+              nb.getAdditional().add(ab);
+            }
+          }
           base.setBinding(nb); 
         } else if (trimDifferential)
           derived.setBinding(null);
@@ -2790,6 +2799,42 @@ public class ProfileUtilities extends TranslatingUtilities {
     //updateURLs(url, webUrl, dest);
   }
 
+  private void mergeAdditionalBinding(ElementDefinitionBindingAdditionalComponent dest, ElementDefinitionBindingAdditionalComponent source) {
+    for (UsageContext t : source.getUsage()) {
+      if (!hasUsage(dest, t)) {
+        dest.addUsage(t);
+      }
+    }
+    if (source.getAny()) {
+      source.setAny(true);
+    }
+    if (source.hasShortDoco()) {
+      dest.setShortDoco(source.getShortDoco());
+    }
+    if (source.hasDocumentation()) {
+      dest.setDocumentation(source.getDocumentation());
+    }
+    
+  }
+
+  private boolean hasUsage(ElementDefinitionBindingAdditionalComponent dest, UsageContext tgt) {
+    for (UsageContext t : dest.getUsage()) {
+      if (t.getCode() != null && t.getCode().matches(tgt.getCode()) && t.getValue() != null && t.getValue().equals(tgt.getValue())) {
+        return true;
+      }
+    }
+    return false;
+  }
+
+  private ElementDefinitionBindingAdditionalComponent getMatchingAdditionalBinding(ElementDefinitionBindingComponent nb,ElementDefinitionBindingAdditionalComponent ab) {
+    for (ElementDefinitionBindingAdditionalComponent t : nb.getAdditional()) {
+      if (t.getValueSet() != null && t.getValueSet().equals(ab.getValueSet()) && t.getPurpose() == ab.getPurpose()) {
+        return t;
+      }
+    }
+    return null;
+  }
+
   private void mergeExtensions(Element tgt, Element src) {
      tgt.getExtension().addAll(src.getExtension());
   }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/FmlParser.java

@@ -422,7 +422,7 @@ public class FmlParser extends ParserBase {
     lexer.token("(");
     boolean done = false;
     while (!done) {
-      parseParameter(ref, lexer);
+      parseParameter(ref, lexer, false);
       done = !lexer.hasToken(",");
       if (!done)
         lexer.next();
@@ -527,7 +527,7 @@ public class FmlParser extends ParserBase {
       target.makeElement("transform").markLocation(loc).setValue(name);
       lexer.token("(");
       if (target.getChildValue("transform").equals(StructureMapTransform.EVALUATE.toCode())) {
-        parseParameter(target, lexer);
+        parseParameter(target, lexer, true);
         lexer.token(",");
         loc = lexer.getCurrentLocation();
         ExpressionNode node = fpe.parse(lexer);
@@ -535,7 +535,7 @@ public class FmlParser extends ParserBase {
         target.addElement("parameter").markLocation(loc).makeElement("valueString").setValue(node.toString());
       } else {
         while (!lexer.hasToken(")")) {
-          parseParameter(target, lexer);
+          parseParameter(target, lexer, true);
           if (!lexer.hasToken(")"))
             lexer.token(",");
         }
@@ -568,9 +568,9 @@ public class FmlParser extends ParserBase {
     }
   }
 
-  private void parseParameter(Element ref, FHIRLexer lexer) throws FHIRLexerException, FHIRFormatError {
+  private void parseParameter(Element ref, FHIRLexer lexer, boolean isTarget) throws FHIRLexerException, FHIRFormatError {
     boolean r5 = VersionUtilities.isR5Plus(context.getVersion());
-    String name = r5 ? "parameter" : "variable";
+    String name = r5 || isTarget ? "parameter" : "variable";
     if (ref.hasChildren(name) && !ref.getChildByName(name).isList()) {
       throw lexer.error("variable on target is not a list, so can't add an element");
     } else if (!lexer.isConstant()) {

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/ParserBase.java

@@ -143,9 +143,12 @@ public abstract class ParserBase {
 	
 	protected StructureDefinition getDefinition(List<ValidationMessage> errors, int line, int col, String ns, String name) throws FHIRFormatError {
 	  if (logical != null) {
-	    String expectedName = ToolingExtensions.readStringExtension(logical, "http://hl7.org/fhir/StructureDefinition/elementdefinition-name");
+	    String expectedName = ToolingExtensions.readStringExtension(logical, "http://hl7.org/fhir/StructureDefinition/elementdefinition-xml-name");
 	    if (expectedName == null) {
 	      expectedName = logical.getType();
+	      if (Utilities.isAbsoluteUrl(expectedName)) {
+	        expectedName = expectedName.substring(expectedName.lastIndexOf("/")+1);
+	      }
 	    }
 	    String expectedNamespace = ToolingExtensions.readStringExtension(logical, "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace");
 	    if (matchesNamespace(expectedNamespace, ns) && matchesName(expectedName, name)) {

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/XmlParser.java

@@ -38,7 +38,9 @@ import java.io.OutputStream;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Comparator;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
@@ -361,10 +363,16 @@ public class XmlParser extends ParserBase {
           if (property.getName().equals("value") && element.isPrimitive())
             element.setValue(av);
           else {
-            Element n = new Element(property.getName(), property, property.getType(), av).markLocation(line, col);
+            String[] vl = {av};
+            if (property.isList() && av.contains(" ")) {
+              vl = av.split(" ");
+            }
+            for (String v : vl) {
+              Element n = new Element(property.getName(), property, property.getType(), v).markLocation(line, col);
               n.setPath(element.getPath()+"."+property.getName());
               element.getChildren().add(n);
             }
+          }
         } else {
           boolean ok = false;
           if (FormatUtilities.FHIR_NS.equals(node.getNamespaceURI())) {
@@ -739,11 +747,20 @@ public class XmlParser extends ParserBase {
       }
     } else {
       setXsiTypeIfIsTypeAttr(xml, element);
+      Set<String> handled = new HashSet<>();
       for (Element child : element.getChildren()) {
-        if (isAttr(child.getProperty()) && wantCompose(element.getPath(), child)) {
+        if (!handled.contains(child.getName()) && isAttr(child.getProperty()) && wantCompose(element.getPath(), child)) {
+          handled.add(child.getName());
+          String av = child.getValue();
+          if (child.getProperty().isList()) {
+            for (Element c2 : element.getChildren()) {
+              if (c2 != child && c2.getName().equals(child.getName())) {
+                av = av + " "+c2.getValue();
+              }
+            }            
+          }
           if (linkResolver != null)
             xml.link(linkResolver.resolveType(child.getType()));
-          String av = child.getValue();
           if (ToolingExtensions.hasExtension(child.getProperty().getDefinition(), ToolingExtensions.EXT_DATE_FORMAT))
             av = convertForDateFormatToExternal(ToolingExtensions.readStringExtension(child.getProperty().getDefinition(), ToolingExtensions.EXT_DATE_FORMAT), av);
           xml.attribute(child.getProperty().getXmlNamespace(),child.getProperty().getXmlName(), av);

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

@@ -186,6 +186,18 @@ public class AdditionalBindingsRenderer {
     return abr;
   }
 
+  protected AdditionalBindingDetail additionalBinding(ElementDefinitionBindingAdditionalComponent ab) {
+    AdditionalBindingDetail abr = new AdditionalBindingDetail();
+    abr.purpose =  ab.getPurpose().toCode();
+    abr.valueSet =  ab.getValueSet();
+    abr.doco =  ab.getDocumentation();
+    abr.docoShort =  ab.getShortDoco();
+    abr.usage = ab.hasUsage() ? ab.getUsageFirstRep() : null;
+    abr.any = ab.getAny();
+    abr.isUnchanged = ab.hasUserData(ProfileUtilities.UD_DERIVATION_EQUALS);
+    return abr;
+  }
+
   public String render() throws IOException {
     if (bindings.isEmpty()) {
       return "";
@@ -455,4 +467,40 @@ public class AdditionalBindingsRenderer {
     
   }
 
+  public void seeAdditionalBindings(ElementDefinition definition, ElementDefinition compDef, boolean compare) {
+    HashMap<String, AdditionalBindingDetail> compBindings = new HashMap<String, AdditionalBindingDetail>();
+    if (compare && compDef.getBinding().getAdditional() != null) {
+      for (ElementDefinitionBindingAdditionalComponent ab : compDef.getBinding().getAdditional()) {
+        AdditionalBindingDetail abr = additionalBinding(ab);
+        if (compBindings.containsKey(abr.getKey())) {
+          abr.incrementCount();
+        }
+        compBindings.put(abr.getKey(), abr);
+      }
+    }
+
+    for (ElementDefinitionBindingAdditionalComponent ab : definition.getBinding().getAdditional()) {
+      AdditionalBindingDetail abr = additionalBinding(ab);
+      if (compare && compDef != null) {
+        AdditionalBindingDetail match = null;
+        do {
+          match = compBindings.get(abr.getKey());
+          if (abr.alreadyMatched())
+            abr.incrementCount();
+        } while (match!=null && abr.alreadyMatched());
+        if (match!=null)
+          abr.setCompare(match);
+        bindings.add(abr);
+        if (abr.compare!=null)
+          compBindings.remove(abr.compare.getKey());
+      } else
+        bindings.add(abr);
+    }
+    for (AdditionalBindingDetail b: compBindings.values()) {
+      b.removed = true;
+      bindings.add(b);
+    }
+    
+  }
+
 }

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

@@ -68,6 +68,7 @@ import org.hl7.fhir.r5.model.UriType;
 import org.hl7.fhir.r5.model.ValueSet;
 import org.hl7.fhir.r5.renderers.utils.BaseWrappers.ResourceWrapper;
 import org.hl7.fhir.r5.renderers.StructureDefinitionRenderer.InternalMarkdownProcessor;
+import org.hl7.fhir.r5.renderers.StructureDefinitionRenderer.SourcedElementDefinition;
 import org.hl7.fhir.r5.renderers.utils.RenderingContext;
 import org.hl7.fhir.r5.renderers.utils.RenderingContext.GenerationRules;
 import org.hl7.fhir.r5.renderers.utils.RenderingContext.KnownLinkType;
@@ -157,6 +158,25 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
   //
   //  }
 
+  public class SourcedElementDefinition {
+    private StructureDefinition profile;
+    private ElementDefinition definition;
+    
+    
+    protected SourcedElementDefinition(StructureDefinition profile, ElementDefinition definition) {
+      super();
+      this.profile = profile;
+      this.definition = definition;
+    }
+    public StructureDefinition getProfile() {
+      return profile;
+    }
+    public ElementDefinition getDefinition() {
+      return definition;
+    }
+    
+  }
+
   public class InternalMarkdownProcessor implements IMarkdownProcessor {
 
     @Override
@@ -1320,6 +1340,22 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
             }
           }
         }
+        if (logicalModel) {
+          List<SourcedElementDefinition> ancestors = new ArrayList<>();
+          getAncestorElements(profile, ancestors);
+          if (ancestors.size() > 0) {
+            c.addPiece(gen.new Piece("br"));
+            c.addPiece(gen.new Piece(null, "Elements defined in Ancestors: ", null));
+            boolean first = true;
+            for (SourcedElementDefinition ed : ancestors) {
+              if (first)
+                first = false;
+              else
+                c.addPiece(gen.new Piece(null, ", ", null));
+              c.addPiece(gen.new Piece(ed.getProfile().getWebPath(), (isAttr(ed) ? "@" : "")+ed.getDefinition().getName(), ed.getDefinition().getDefinition()));
+            }     
+          }
+        }
       }
       if (definition.getPath().endsWith("url") && definition.hasFixed()) {
         c.getPieces().add(checkForNoChange(definition.getFixed(), gen.new Piece(null, "\""+buildJson(definition.getFixed())+"\"", null).addStyle("color: darkgreen")));
@@ -1552,6 +1588,7 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
             } 
 
             AdditionalBindingsRenderer abr = new AdditionalBindingsRenderer(context.getPkp(), corePath, profile, definition.getPath(), rc, null, this);
+            abr.seeAdditionalBindings(definition, null, false);
             if (binding.hasExtension(ToolingExtensions.EXT_MAX_VALUESET)) {
               abr.seeMaxBinding(ToolingExtensions.getExtension(binding, ToolingExtensions.EXT_MAX_VALUESET));
             }
@@ -1651,6 +1688,26 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
     return c;
   }
 
+  private boolean isAttr(SourcedElementDefinition ed) {
+    for (Enumeration<PropertyRepresentation> t : ed.getDefinition().getRepresentation()) {
+      if (t.getValue() == PropertyRepresentation.XMLATTR) {
+        return true;
+      }
+    }
+    return false;
+  }
+
+  private void getAncestorElements(StructureDefinition profile, List<SourcedElementDefinition> ancestors) {
+    StructureDefinition base = context.getContext().fetchResource(StructureDefinition.class, profile.getBaseDefinition());
+    if (base != null) {
+      getAncestorElements(base, ancestors);
+      for (ElementDefinition ed : base.getDifferential().getElement()) {
+        if (Utilities.charCount(ed.getPath(), '.') == 1) {
+          ancestors.add(new SourcedElementDefinition(base, ed));
+        }
+      }
+    }
+  }
 
   private void addCanonicalListExt(HierarchicalTableGenerator gen, Cell c, List<Extension> list, String start, boolean bold) {
     List<CanonicalType> clist = new ArrayList<>();

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/validation/ValueSetValidator.java

@@ -686,6 +686,9 @@ public class ValueSetValidator extends ValueSetProcessBase {
 
   private ValidationResult validateCode(String path, Coding code, CodeSystem cs, CodeableConcept vcc, ValidationProcessInfo info) {
     ConceptDefinitionComponent cc = cs.hasUserData("tx.cs.special") ? ((SpecialCodeSystem) cs.getUserData("tx.cs.special")).findConcept(code) : findCodeInConcept(cs.getConcept(), code.getCode(), allAltCodes);
+    if (cc == null) {
+      cc = findSpecialConcept(code, cs);
+    }
     if (cc == null) {
       if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
         String msg = context.formatMessage(I18nConstants.UNKNOWN_CODE__IN_FRAGMENT, code.getCode(), cs.getVersionedUrl());
@@ -759,6 +762,28 @@ public class ValueSetValidator extends ValueSetProcessBase {
     }
   }
 
+  private ConceptDefinitionComponent findSpecialConcept(Coding c, CodeSystem cs) {
+    // handling weird special cases in v2 code systems 
+    if ("http://terminology.hl7.org/CodeSystem/v2-0203".equals(cs.getUrl())) {
+      String code = c.getCode();
+      if (code != null && code.startsWith("NN") && code.length() > 3) {
+        ConceptDefinitionComponent cd = findCountryCode(code.substring(2));
+        if (cd != null) {
+          return new ConceptDefinitionComponent(code).setDisplay("National Identifier for "+cd.getDisplay());
+        }
+      }      
+    }
+//    0396: HL7nnnn, IBTnnnn, ISOnnnn, X12Dennnn, 99zzz
+//    0335: PRNxxx
+    return null;
+  }
+
+  
+  private ConceptDefinitionComponent findCountryCode(String code) {
+    ValidationResult vr = context.validateCode(new ValidationOptions(), "urn:iso:std:iso:3166", null, code, null);
+    return vr == null || !vr.isOk() ? null : new ConceptDefinitionComponent(code).setDisplay(vr.getDisplay()).setDefinition(vr.getDefinition());
+  }
+
   private IssueSeverity dispWarning() {
     return options.isDisplayWarningMode() ? IssueSeverity.WARNING : IssueSeverity.ERROR; 
   }
@@ -811,15 +836,6 @@ public class ValueSetValidator extends ValueSetProcessBase {
     return null;
   }
 
-  private String gen(Coding code) {
-    if (code.hasSystem()) {
-      return code.getSystem()+"#"+code.getCode();
-    } else {
-      return null;
-    }
-  }
-
-
   private String getValueSetSystemOrNull() throws FHIRException {
     if (valueset == null) {
       return null;

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/CommonPackages.java

@@ -6,6 +6,6 @@ public class CommonPackages {
   public static final String VER_XVER = "0.0.12";
   
   public static final String ID_PUBPACK = "hl7.fhir.pubpack";
-  public static final String VER_PUBPACK = "0.1.5";
+  public static final String VER_PUBPACK = "0.1.6";
 
 }

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

@@ -394,10 +394,10 @@ Does_not_match_slice_ = Does not match slice ''{0}'' (discriminator: {1})
 Profile__does_not_match_for__because_of_the_following_profile_issues__ = Profile {0} does not match for {1} because of the following profile issues: {2}
 This_element_does_not_match_any_known_slice_ = This element does not match any known slice {0}
 defined_in_the_profile = Defined in the profile
-This_does_not_appear_to_be_a_FHIR_resource_unknown_name_ = This does not appear to be a FHIR resource (unknown name ''{0}'')
+This_does_not_appear_to_be_a_FHIR_resource_unknown_name_ = This content cannot be parsed (unknown or unrecognised XML root element name ''{0}'')
-This_cannot_be_parsed_as_a_FHIR_object_no_name = This cannot be parsed as a FHIR object (no name)
+This_cannot_be_parsed_as_a_FHIR_object_no_name = This content cannot be parsed (no name)
-This_does_not_appear_to_be_a_FHIR_resource_unknown_namespacename_ = This does not appear to be a FHIR resource (unknown namespace/name ''{0}::{1}'')
+This_does_not_appear_to_be_a_FHIR_resource_unknown_namespacename_ = This content cannot be parsed (unknown or unrecognised XML Root element namespace/name ''{0}::{1}'')
-This__cannot_be_parsed_as_a_FHIR_object_no_namespace = This ''{0}'' cannot be parsed as a FHIR object (no namespace)
+This__cannot_be_parsed_as_a_FHIR_object_no_namespace = This ''{0}'' cannot be parsed (no namespace on the XML Root element)
 Unable_to_find_resourceType_property = Unable to find resourceType property
 Error_parsing_JSON_the_primitive_value_must_be_a_string = Error parsing JSON: the primitive value must be a string
 Error_parsing_JSON_the_primitive_value_must_be_a_number = Error parsing JSON: the primitive value must be a number

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/StructureMapValidator.java

@@ -1169,7 +1169,7 @@ public class StructureMapValidator extends BaseValidator {
             Element g = (Element) grp.getTargetGroup().getUserData("element.source");
             if (g.hasUserData("structuremap.parameters")) {
               VariableSet pvars = (VariableSet) g.getUserData("structuremap.parameters");
-              rule(errors, "2023-03-01", IssueType.INVALID, dependent.line(), dependent.col(), stack.getLiteralPath(), pvars.matches(lvars), I18nConstants.SM_DEPENDENT_PARAM_TYPE_MISMATCH_DUPLICATE, grp.getTargetGroup().getName(), pvars.summary(), lvars.summary());
+              warning(errors, "2023-03-01", IssueType.INVALID, dependent.line(), dependent.col(), stack.getLiteralPath(), pvars.matches(lvars), I18nConstants.SM_DEPENDENT_PARAM_TYPE_MISMATCH_DUPLICATE, grp.getTargetGroup().getName(), pvars.summary(), lvars.summary());
             } else {
               g.setUserData("structuremap.parameters", lvars);
             }

org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.validation/4.0.1/iso3166.cache

@@ -163,6 +163,27 @@ v: {
   "code" : "US",
   "system" : "urn:iso:std:iso:3166",
   "version" : "2018",
+  "issues" : {
+  "resourceType" : "OperationOutcome"
+}
+
+}
+-------------------------------------------------------------------------------------
+{"code" : {
+  "system" : "urn:iso:std:iso:3166",
+  "code" : "FIN"
+}, "valueSet" :null, "langs":"", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"true", "profile": {
+  "resourceType" : "Parameters",
+  "parameter" : [{
+    "name" : "profile-url",
+    "valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
+  }]
+}}####
+v: {
+  "display" : "Finland",
+  "code" : "FIN",
+  "system" : "urn:iso:std:iso:3166",
+  "version" : "2018",
   "unknown-systems" : "",
   "issues" : {
   "resourceType" : "OperationOutcome"