Merge branch 'main' into version-iri-fix

build.gradle.kts

@@ -7,7 +7,7 @@ plugins {
 }
 
 group = "org.hl7.fhir"
-version = "1.9.1-SNAPSHOT"
+version = "1.9.2-SNAPSHOT"
 
 java {
     withJavadocJar()

gradle.properties

@@ -1,4 +1,4 @@
-fhirCoreVersion = 6.2.15-SNAPSHOT
+fhirCoreVersion = 6.3.2
 apachePoiVersion = 5.2.1
 jacksonVersion = 2.16.0
 apacheHttpcomponentsVersion = 4.5.13

src/main/java/org/hl7/fhir/definitions/generators/specification/TerminologyNotesGenerator.java

@@ -225,9 +225,9 @@ else if (name.equals("FHIRAllTypes"))
             }
           }
         } else if (cd.getBinding() == BindingSpecification.BindingMethod.ValueSet) {
-          if (Utilities.noString(cd.getReference())) 
-            write("??");
-          else if (cd.getReference().startsWith("valueset-"))
+          if (Utilities.noString(cd.getReference())) {
+            System.out.println("no value set for "+cd.getName());
+          } else if (cd.getReference().startsWith("valueset-"))
             write("<a href=\""+prefix+cd.getReference()+".html\">http://hl7.org/fhir/ValueSet/"+cd.getReference().substring(9)+"</a><!-- a -->");            
           else if (cd.getReference().startsWith("http://hl7.org/fhir")) {
             if (cd.getReference().startsWith("http://terminology.hl7.org/ValueSet/v3-")) {

src/main/java/org/hl7/fhir/tools/publisher/ExampleInspector.java

@@ -10,6 +10,7 @@
 import java.util.ArrayList;
 import java.util.EnumSet;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Locale;
 import java.util.Map;
@@ -651,7 +652,6 @@ else if (SIDUtilities.isKnownSID(url) || Utilities.existsInList(url, "http://hl7
       return true;
   }
 
-
   @Override
   public IValidatorResourceFetcher setLocale(Locale locale) {
     // don't need to do anything here 
@@ -669,7 +669,7 @@ public byte[] fetchRaw(IResourceValidator validator, String source) throws Malfo
 
 
   @Override
-  public CanonicalResource fetchCanonicalResource(IResourceValidator validator, String url) throws URISyntaxException {
+  public CanonicalResource fetchCanonicalResource(IResourceValidator validator, Object appContext, String url) throws URISyntaxException {
     for (CanonicalResource t : context.fetchResourcesByType(CanonicalResource.class)) {
       if (t.getUrl().equals(url)) {
         return t;
@@ -863,6 +863,11 @@ public boolean paramIsType(String name, int index) {
     throw new NotImplementedException();
   }
 
+  @Override
+  public Set<String> fetchCanonicalResourceVersions(IResourceValidator validator, Object appContext, String url) {
+    return new HashSet<>();
+  }
+
 
 }
 

src/main/java/org/hl7/fhir/tools/publisher/PageProcessor.java

@@ -75,6 +75,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
 import org.hl7.fhir.convertors.SpecDifferenceEvaluator;
 import org.hl7.fhir.convertors.TypeLinkProvider;
 import org.hl7.fhir.convertors.loaders.loaderR5.R4ToR5Loader;
+import org.hl7.fhir.convertors.loaders.loaderR5.R5ToR5Loader;
 import org.hl7.fhir.definitions.Config;
 import org.hl7.fhir.definitions.generators.specification.BaseGenerator;
 import org.hl7.fhir.definitions.generators.specification.DataTypeTableGenerator;
@@ -479,6 +480,7 @@ public int compare(String arg0, String arg1) {
   private String webLocation;
   private String searchLocation;
   private String extensionsLocation;
+  private long maxMemory = 0;
 
   private String getComputerName()
   {
@@ -10446,10 +10448,10 @@ public void setDefinitions(Definitions definitions) throws Exception {
     workerContext.setAllowLoadingDuplicates(true);
     log("Load UTG Terminology", LogMessageType.Process);
     utg = new FilesystemPackageCacheManager.Builder().build().loadPackage("hl7.terminology");
-    workerContext.loadFromPackage(utg, new R4ToR5Loader(BuildWorkerContext.defaultTypesToLoad(), new UTGLoader(utg.version()), workerContext.getVersion()));
+    workerContext.loadFromPackage(utg, new R5ToR5Loader(BuildWorkerContext.defaultTypesToLoad(), new UTGLoader(utg.version())));
     log("Load Extensions", LogMessageType.Process);
     ext = new FilesystemPackageCacheManager.Builder().build().loadPackage("hl7.fhir.uv.extensions", "current");
-    workerContext.loadFromPackage(ext, new R4ToR5Loader(BuildWorkerContext.extensionTypesToLoad(), new ExtensionsLoader(ext.version(), extensionsLocation), workerContext.getVersion()));
+    workerContext.loadFromPackage(ext, new R5ToR5Loader(BuildWorkerContext.extensionTypesToLoad(), new ExtensionsLoader(ext.version(), extensionsLocation)));
     log("Load DICOM Terminology", LogMessageType.Process);
     dicom = new FilesystemPackageCacheManager.Builder().build().loadPackage("fhir.dicom");
     workerContext.loadFromPackage(dicom, new R4ToR5Loader(BuildWorkerContext.defaultTypesToLoad(), new DICOMLoader(utg.version()), workerContext.getVersion()));
@@ -10530,6 +10532,16 @@ public void log(String content, LogMessageType type) {
       System.out.println(String.format("%1$-74s", content)+" "+String.format("%1$8s", Float.toString(gap))+" "+String.format("%1$3s", Long.toString(secs))+"sec "+String.format("%1$4s", Long.toString(used))+"MB");
     } else
       System.out.println(content);
+
+
+    Runtime runtime = Runtime.getRuntime();
+    long totalMemory = runtime.totalMemory();
+    long freeMemory = runtime.freeMemory();
+    long usedMemory = totalMemory - freeMemory;
+    if (usedMemory > maxMemory) {
+      maxMemory = usedMemory;
+    }
+
   }
 
 //  public void logNoEoln(String content) {
@@ -12442,4 +12454,10 @@ public String processMarkdown(String location, String text) throws FHIRException
       throw new FHIRException(e);
     }
   }
+
+  public long getMaxMemory() {
+    return maxMemory;
+  }
+
+
 }

src/main/java/org/hl7/fhir/tools/publisher/Publisher.java

@@ -824,6 +824,7 @@ public void execute(String folder, String[] args) throws IOException {
       if (isGenerate && buildFlags.get("all"))
         produceQA();
 
+      page.log("Max Memory Used = "+Utilities.describeSize(page.getMaxMemory()), LogMessageType.Process);
       if (!buildFlags.get("all")) {
         page.log("This was a Partial Build", LogMessageType.Process);
         CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
@@ -1871,13 +1872,13 @@ private void addTypes(CodeSystem cs, StructureDefinition sd, List<ConceptDefinit
     cd.setDisplay(sd.getType());
     cd.setDefinition(sd.getDescription());
     if (!sd.getType().equals("Base")) {
-      CodeSystemUtilities.setProperty(cs, cd, "kind", new CodeType(codeForKind(sd)));
+      CodeSystemUtilities.setProperty(cs, cd, "http://hl7.org/fhir/type-properties#kind", "kind", new CodeType(codeForKind(sd)));
     }
     if (sd.getAbstract()) {
-      CodeSystemUtilities.setProperty(cs, cd, "abstract-type", new BooleanType(true));
+      CodeSystemUtilities.setProperty(cs, cd, "http://hl7.org/fhir/type-properties#abstract-type", "abstract-type", new BooleanType(true));
     }
     if (sd.hasExtension(ToolingExtensions.EXT_RESOURCE_INTERFACE)) {
-      CodeSystemUtilities.setProperty(cs, cd, "interface", new BooleanType(true));
+      CodeSystemUtilities.setProperty(cs, cd, "http://hl7.org/fhir/type-properties#interface", "interface", new BooleanType(true));
     }
     list.add(cd);
     for (StructureDefinition t : types) {
@@ -5269,21 +5270,24 @@ private void processExample(Example e, ResourceDefn resn, StructureDefinition pr
           }
         }
       }
-      if (e.getResource() == null && e.getElement() == null) {
-        String xml = XMLUtil.elementToString(e.getXml().getDocumentElement()).replace("<?xml version=\"1.0\" encoding=\"UTF-16\"?>", "").trim();
-        e.setElement(new Manager().parseSingle(page.getWorkerContext(), new StringInputStream(xml), FhirFormat.XML));
-        e.setResource(new XmlParser().parse(xml));
-      }
     } catch (Throwable ex) {
       StringWriter errors = new StringWriter();
       System.out.println("Error generating narrative for example "+e.getName()+": "+ex.getMessage());
-//      ex.printStackTrace();
+      ex.printStackTrace();
       XhtmlNode xhtml = new XhtmlNode(NodeType.Element, "div");
       xhtml.addTag("p").setAttribute("style", "color: maroon").addText("Error processing narrative: " + ex.getMessage());
       xhtml.addTag("p").setAttribute("style", "color: maroon").addText(errors.toString());
       narrative = new XhtmlComposer(XhtmlComposer.HTML).compose(xhtml);
     }
-
+    try {
+      if (e.getResource() == null && e.getElement() == null) {
+        String xml = XMLUtil.elementToString(e.getXml().getDocumentElement()).replace("<?xml version=\"1.0\" encoding=\"UTF-16\"?>", "").trim();
+        e.setElement(new Manager().parseSingle(page.getWorkerContext(), new StringInputStream(xml), FhirFormat.XML));
+        e.setResource(new XmlParser().parse(xml));
+      }
+    } catch (Throwable ex) {
+      System.out.println("Error reparsing example "+e.getName()+": "+ex.getMessage());
+    }
     if (rt.equals("ValueSet")) {
       try {
         ValueSet vs = (ValueSet) loadExample(file);