Merge remote-tracking branch 'origin/master' into do-20240122-base-en…

…gine
hapifhir · Jun 17, 2024 · fbf2d01 · fbf2d01
2 parents b24fb10 + b970653
commit fbf2d01
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Showing 44 changed files with 1,787 additions and 788 deletions.
diff --git a/i18n-coverage-table.png b/i18n-coverage-table.png
diff --git a/i18n-coverage.csv b/i18n-coverage.csv
@@ -1,5 +1,5 @@
 Locale,Coverage #,Coverage %
 de,835,42%
 es,718,36%
-ja,906,46%
+ja,906,45%
 nl,1376,69%
diff --git a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/ContextUtilities.java b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/ContextUtilities.java
@@ -453,5 +453,16 @@ public boolean isAbstractType(String typeName) {
     return false;
   }
 
+  public boolean isDomainResource(String typeName) {
+    StructureDefinition sd = context.fetchTypeDefinition(typeName);
+    while (sd != null) {
+      if ("DomainResource".equals(sd.getType())) {
+        return true;
+      }
+      sd = context.fetchResource(StructureDefinition.class, sd.getBaseDefinition());  
+    }
+    return false;
+  }
+
 }
 
diff --git a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/SimpleWorkerContext.java b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/SimpleWorkerContext.java
@@ -806,7 +806,21 @@ public boolean hasPackage(String id, String ver) {
   }
 
   public boolean hasPackage(String idAndver) {
-    return loadedPackages.contains(idAndver);
+    if (loadedPackages.contains(idAndver)) {
+      return true;
+    }
+    // not clear whether the same logic should apply to other cross-version packages?
+    if (idAndver.startsWith("hl7.fhir.uv.extensions")) {
+      String v = idAndver.substring(idAndver.lastIndexOf("#")+1);
+      for (String s : loadedPackages) {
+        String v2 = s.substring(s.lastIndexOf("#")+1);
+        if (s.startsWith("hl7.fhir.uv.extensions.") && VersionUtilities.versionsMatch(v, v2)) {
+          return true;
+        }
+      }
+    }
+    return false;
+
   }
 
   @Override

diff --git a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/JsonParser.java b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/JsonParser.java
@@ -779,7 +779,7 @@ public void compose(Element e, OutputStream stream, OutputStyle style, String id
     prop("resourceType", e.getType(), null);
     Set<String> done = new HashSet<String>();
     for (Element child : e.getChildren()) {
-      compose(e.getName(), e, done, child);
+      compose(e.getName(), e, done, child, "");
     }
     json.endObject();
     json.finish();
@@ -804,28 +804,28 @@ public void compose(Element e, JsonCreator json) throws Exception {
     prop("resourceType", e.getType(), linkResolver == null ? null : linkResolver.resolveProperty(e.getProperty()));
     Set<String> done = new HashSet<String>();
     for (Element child : e.getChildren()) {
-      compose(e.getName(), e, done, child);
+      compose(e.getName(), e, done, child, "");
     }
     json.endObject();
     json.finish();
   }
 
-  private void compose(String path, Element e, Set<String> done, Element child) throws IOException {
+  private void compose(String path, Element e, Set<String> done, Element child, String tgtPath) throws IOException {
     checkComposeComments(child);
     if (wantCompose(path, child)) {
       boolean isList = child.hasElementProperty() ? child.getElementProperty().isList() : child.getProperty().isList();
       if (!isList) {// for specials, ignore the cardinality of the stated type
-        compose(path, child);
+        compose(path, child, tgtPath);
       } else if (!done.contains(child.getName())) {
         done.add(child.getName());
         List<Element> list = e.getChildrenByName(child.getName());
-        composeList(path, list);
+        composeList(path, list, tgtPath);
       }
     }
   }
 
 
-  private void composeList(String path, List<Element> list) throws IOException {
+  private void composeList(String path, List<Element> list, String tgtPath) throws IOException {
     // there will be at least one element
     String name = list.get(0).getName();
     boolean complex = true;
@@ -858,6 +858,7 @@ private void composeList(String path, List<Element> list) throws IOException {
     }
     if (complex) {
       openArray(name, linkResolver == null ? null : linkResolver.resolveProperty(list.get(0).getProperty()));
+      int i = 0;
       for (Element item : list) {
         if (item.hasChildren()) {
           open(null,null);
@@ -872,11 +873,21 @@ private void composeList(String path, List<Element> list) throws IOException {
           }
           Set<String> done = new HashSet<String>();
           for (Element child : item.getChildren()) {
-            compose(path+"."+name+"[]", item, done, child);
+            String tp = tgtPath;
+            if (child.getSpecial() == SpecialElement.BUNDLE_ENTRY) {
+              if (Utilities.noString(tp)) {
+                tp = "Bnd."+i+".";
+              } else {
+                tp = tgtPath+i+".";
+              }
+            }
+            compose(path+"."+name+"[]", item, done, child, tp);
           }
           close();
-        } else
+        } else {
           json.nullValue();
+        }
+        i++;
       }
       closeArray();
     }
@@ -903,14 +914,14 @@ else if (Utilities.existsInList(type, "decimal"))
       json.value(item.getValue());
   }
 
-  private void compose(String path, Element element) throws IOException {
+  private void compose(String path, Element element, String tgtPath) throws IOException {
     String name = element.getName();
     if (element.isPrimitive() || isPrimitive(element.getType())) {
       if (element.hasValue())
         primitiveValue(name, element);
       name = "_"+name;
       if (element.getType().equals("xhtml"))
-        json.anchor("end-xhtml");
+        json.anchor(tgtPath+"end-xhtml");
     }
     if (element.hasChildren()) {
       open(name, linkResolver == null ? null : linkResolver.resolveProperty(element.getProperty()));
@@ -925,7 +936,7 @@ private void compose(String path, Element element) throws IOException {
       }
       Set<String> done = new HashSet<String>();
       for (Element child : element.getChildren()) {
-        compose(path+"."+element.getName(), element, done, child);
+        compose(path+"."+element.getName(), element, done, child, tgtPath);
       }
       close();
     }

diff --git a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/XmlParser.java b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/XmlParser.java
@@ -100,6 +100,7 @@ public XmlParser(IWorkerContext context) {
   }
 
   private String schemaPath;
+  private int bundleEntryCounter = 0;
 
   public String getSchemaPath() {
     return schemaPath;
@@ -117,10 +118,10 @@ public void setAllowXsiLocation(boolean allowXsiLocation) {
   }
 
   public List<ValidatedFragment> parse(InputStream inStream) throws FHIRFormatError, DefinitionException, FHIRException, IOException {
-    
+
     byte[] content = TextFile.streamToBytes(inStream);
     ValidatedFragment focusFragment = new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "xml", content, false);
-    
+
     ByteArrayInputStream stream = new ByteArrayInputStream(content);
     Document doc = null;
     try {
@@ -318,7 +319,7 @@ private StructureDefinition findLegalConstraint(String xsiType, String actualTyp
     }
     return null;
   }
-  
+
   public Element parse(List<ValidationMessage> errors, org.w3c.dom.Element base, String type) throws Exception {
     StructureDefinition sd = getDefinition(errors, 0, 0, FormatUtilities.FHIR_NS, type);
     Element result = new Element(base.getLocalName(), new Property(context, sd.getSnapshot().getElement().get(0), sd, getProfileUtilities(), getContextUtilities())).setFormat(FhirFormat.XML).setNativeObject(base);
@@ -429,7 +430,7 @@ private void parseChildren(List<ValidationMessage> errors, String path, org.w3c.
     while (child != null) {
       if (child.getNodeType() == Node.ELEMENT_NODE) {
         Property property = getElementProp(properties, child.getLocalName(), child.getNamespaceURI());
-        
+
         if (property != null) {
           if (property.getName().equals(lastName)) {
             repeatCount++;
@@ -507,13 +508,13 @@ private void parseChildren(List<ValidationMessage> errors, String path, org.w3c.
                 lastName = cgProp.getName();
                 repeatCount = 0;
               }
-              
+
               String npath = path+"/"+pathPrefix(cgProp.getXmlNamespace())+cgProp.getName();
               String name = cgProp.getName();
               Element cgn = new Element(cgProp.getName(), cgProp).setFormat(FhirFormat.XML);
               cgn.setPath(element.getPath()+"."+cgProp.getName()+"["+repeatCount+"]"); 
               element.getChildren().add(cgn);
-              
+
               npath = npath+"/"+pathPrefix(child.getNamespaceURI())+child.getLocalName();
               name = child.getLocalName();
               Element n = new Element(name, property).markLocation(line(child, false), col(child, false)).setFormat(FhirFormat.XML).setNativeObject(child);
@@ -534,20 +535,20 @@ private void parseChildren(List<ValidationMessage> errors, String path, org.w3c.
           lastName = cgProp.getName();
           repeatCount = 0;
         }
-        
+
         String npath = path+"/"+pathPrefix(cgProp.getXmlNamespace())+cgProp.getName();
         String name = cgProp.getName();
         Element cgn = new Element(cgProp.getName(), cgProp).setFormat(FhirFormat.XML);
         cgn.setPath(element.getPath()+"."+cgProp.getName()+"["+repeatCount+"]"); 
         element.getChildren().add(cgn);
-        
+
         npath = npath+"/text()";
         name = mtProp.getName();
         Element n = new Element(name, mtProp, mtProp.getType(), child.getTextContent().trim()).markLocation(line(child, false), col(child, false)).setFormat(FhirFormat.XML).setNativeObject(child);
         cgn.getChildren().add(n);
         n.setPath(element.getPath()+"."+mtProp.getName());
 
-        
+
       } else if (child.getNodeType() == Node.CDATA_SECTION_NODE) {
         logError(errors, ValidationMessage.NO_RULE_DATE, line(child, false), col(child, false), path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.CDATA_IS_NOT_ALLOWED), IssueSeverity.ERROR);
       } else if (!Utilities.existsInList(child.getNodeType(), 3, 8)) {
@@ -565,7 +566,7 @@ private Property getChoiceGroupProp(List<Property> properties) {
     }
     return null;
   }
-  
+
   private boolean validAttrValue(String value) {
     if (version == null) {
       return true;
@@ -608,7 +609,7 @@ public int compare(Property o1, Property o2) {
           return p;
       }
     }
-    
+
 
     return null;
   }
@@ -737,7 +738,7 @@ public void compose(Element e, OutputStream stream, OutputStyle style, String ba
     if (hasTypeAttr(e))
       xml.namespace("http://www.w3.org/2001/XMLSchema-instance", "xsi");
     addNamespaces(xml, e);
-    composeElement(xml, e, e.getType(), true);
+    composeElement(xml, e, e.getType(), true, "");
     xml.end();
   }
 
@@ -795,11 +796,11 @@ public void compose(Element e, IXMLWriter xml) throws Exception {
     if (schemaPath != null) {
       xml.setSchemaLocation(FormatUtilities.FHIR_NS, Utilities.pathURL(schemaPath, e.fhirType()+".xsd"));
     }
-    composeElement(xml, e, e.getType(), true);
+    composeElement(xml, e, e.getType(), true, "");
     xml.end();
   }
 
-  private void composeElement(IXMLWriter xml, Element element, String elementName, boolean root) throws IOException, FHIRException {
+  private void composeElement(IXMLWriter xml, Element element, String elementName, boolean root, String tgtPath) throws IOException, FHIRException {
     if (showDecorations) {
       @SuppressWarnings("unchecked")
       List<ElementDecoration> decorations = (List<ElementDecoration>) element.getUserData("fhir.decorations");
@@ -833,7 +834,7 @@ private void composeElement(IXMLWriter xml, Element element, String elementName,
           new CDANarrativeFormat().convert(xml, new XhtmlParser().parseFragment(rawXhtml));
         } else {
           xml.escapedText(rawXhtml);
-          xml.anchor("end-xhtml");
+          xml.anchor(tgtPath+"end-xhtml");
         }
       } else if (isText(element.getProperty())) {
         if (linkResolver != null)
@@ -857,7 +858,7 @@ private void composeElement(IXMLWriter xml, Element element, String elementName,
             }
           }
           for (Element child : element.getChildren()) 
-            composeElement(xml, child, child.getName(), false);
+            composeElement(xml, child, child.getName(), false, tgtPath);
           xml.exit(element.getProperty().getXmlNamespace(),elementName);
         } else
           xml.element(elementName);
@@ -908,8 +909,18 @@ private void composeElement(IXMLWriter xml, Element element, String elementName,
             if (linkResolver != null)
               xml.link(linkResolver.resolveProperty(element.getProperty()));
             xml.text(child.getValue());
-          } else if (!isAttr(child.getProperty()))
-            composeElement(xml, child, child.getName(), false);
+          } else if (!isAttr(child.getProperty())) {
+            String tp = tgtPath;
+            if (child.getSpecial() == SpecialElement.BUNDLE_ENTRY) {
+              bundleEntryCounter ++;
+              if (Utilities.noString(tp)) {
+                tp = "Bnd."+bundleEntryCounter+".";
+              } else {
+                tp = tgtPath+bundleEntryCounter+".";
+              }
+            }
+            composeElement(xml, child, child.getName(), false, tp);
+          }
         }
       }
       if (!root && element.getSpecial() != null)
@@ -924,12 +935,12 @@ private String makeNamespaceAbbrev(Property property, IXMLWriter xml) {
     ElementDefinition ed = property.getDefinition();
     String ns = property.getXmlNamespace();
     String n = property.getXmlName();
-    
+
     String diff = property.getName().toLowerCase().replace(n.toLowerCase(), "");
     if (!Utilities.noString(diff) && diff.length() <= 5 && Utilities.isToken(diff) && !xml.abbreviationDefined(diff)) {
       return diff;
     }
-    
+
     int i = ns.length()-1;
     while (i > 0) {
       if (Character.isAlphabetic(ns.charAt(i)) || Character.isDigit(ns.charAt(i))) {
@@ -942,7 +953,7 @@ private String makeNamespaceAbbrev(Property property, IXMLWriter xml) {
     if (!Utilities.noString(tail) && tail.length() <= 5 && Utilities.isToken(tail) && !xml.abbreviationDefined(tail)) {
       return tail;
     }
-    
+
     i = 0;
     while (xml.abbreviationDefined("ns"+i)) {
       i++;
@@ -1008,17 +1019,17 @@ private String checkHeader(List<ValidationMessage> errors, InputStream stream) t
   class NullErrorHandler implements ErrorHandler {
     @Override
     public void fatalError(SAXParseException e) {
-        // do nothing
+      // do nothing
     }
 
     @Override
     public void error(SAXParseException e) {
-        // do nothing
+      // do nothing
     }
-    
+
     @Override
     public void warning(SAXParseException e) {
-        // do nothing
+      // do nothing
     }
-}
+  }
 }
diff --git a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ProfileDrivenRenderer.java b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ProfileDrivenRenderer.java
@@ -1068,19 +1068,14 @@ private List<PropertyWrapper> splitExtensions(StructureDefinition profile, List<
                 ed = xverManager.makeDefinition(url);
                 new ContextUtilities(getContext().getWorker()).generateSnapshot(ed);
                 getContext().getWorker().cacheResource(ed);
-              }
+              } 
             }
             if (p.getName().equals("modifierExtension") && ed == null) {
               throw new DefinitionException("Unknown modifier extension "+url);
             }
             PropertyWrapper pe = map.get(p.getName()+"["+url+"]");
             if (pe == null) {
               if (ed == null) {
-                if (url != null && url.startsWith("http://hl7.org/fhir") && !url.startsWith("http://hl7.org/fhir/us")) {
-                  if (!ProfileUtilities.isSuppressIgnorableExceptions()) {
-                    throw new DefinitionException("unknown extension "+url);
-                  }
-                }
                 // System.out.println("unknown extension "+url);
                 pe = new PropertyWrapperDirect(this.context, new Property(p.getName()+"["+url+"]", p.getTypeCode(), p.getDefinition(), p.getMinCardinality(), p.getMaxCardinality(), ex), null);
               } else {

diff --git a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ValueSetRenderer.java b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ValueSetRenderer.java
@@ -216,7 +216,7 @@ private boolean generateExpansion(XhtmlNode x, ValueSet vs, boolean header, List
       if (vs.getExpansion().hasTotal()) {
         if (count != vs.getExpansion().getTotal()) {
           x.para().style("border: maroon 1px solid; background-color: #FFCCCC; font-weight: bold; padding: 8px")
-            .addText(context.formatPhrase(hasFragment ? RenderingContext.VALUE_SET_HAS_AT_LEAST : RenderingContext.VALUE_SET_HAS, vs.getExpansion().getTotal()));
+            .addText(context.formatPhrase(hasFragment ? RenderingContext.VALUE_SET_HAS_AT_LEAST : RenderingContext.VALUE_SET_HAS, vs.getExpansion().getTotal(), count));
         } else {
           x.para().tx(context.formatPhrase(hasFragment ? RenderingContext.VALUE_SET_CONTAINS_AT_LEAST : RenderingContext.VALUE_SET_CONTAINS, vs.getExpansion().getTotal()));          
         }